All right, I finally got around to playing this episode, and wow, this is incredibly ambitious! I remember thinking that I was the only one who thought of this idea, but now I see that you've had the same idea since
freaking June! And, apparently, there have been two other projects like this that Emral was a part of, so I guess my idea wasn't that unique after all. Oh well.
AND NOW, MY REVIEW OF MARIO PRIME:
The first thing I'd like to point out is that the episode's in-game name is shortened to "Mario Prime - The Saga" so that it doesn't go off screen, and that's something I haven't seen until now.
So, like I wrote earlier, this is ambitious, but it's also a bit disappointing. The entire episode is styled after Metroid and Castlevania games in that it has a few large areas that are interconnected and contain multiple save spots, but unlike those two games, the episode is completely linear. Sure, the Metroid and Castlevania games are also linear to an extent, but those games also reward exploration. A good example would be the Screw Attack in the first Metroid game: it's probably the most iconic power-up in Metroid, but it is absolutely optional in the NES Metroid; the entire game can be beaten without it. In this episode, not only are all of the stars required, but they have to be collected in a specific order (with the exception of one pair of stars that can only switch places with each other). If the path splits, then either the player is unable to reach one path and must go the other or the player has already explored one path and now has no reason to go though that path again (unless it contains another split path that hasn't yet been traversed), meaning he/she will go to the other path. Heck, the only power-up in the episode is the mushroom, and that alone eliminates quite a lot of potential possibilities for exploration, even if the power-ups were just guarded by star doors like a generic bonus level. In other words, it's just a linear episode wearing the skin of a nonlinear episode, and I believe that much, much more can be done with the concept than what this episode demonstrates.
Anyway, the episode begins with a really well made introductory level which does a good job at establishing the story and the world, except for one minor plot hole I came across:
What do you mean "the sun is not rising anymore"? The sky is blue! IT'S OBVIOUSLY FREAKING DAYTIME!

Also, "cannot" is actually only one word, not two. By the way, why is the Maleficent Mask a saw blade sprite-swap? Saw blades make that annoying "tik-tik-tik-tik-tik-tik-tik" noise constantly while on screen, so the least you could do is make the text boxes appear instantly after the previous one instead of giving them that short delay.
Anyway, after the story part of the introductory level is the mandatory-tutorial part of the introductory level, which is quite annoying for those of us who already know how SMBX works. Yes, I know that hitting a switch block will turn dashed blocks into solid blocks, and I think that anyone can figure that out pretty quickly even if you don't explain it. To be fair, I would not have realized that the glowing pots were actually ? block sprite-swaps or that the golden pipes have Allow NPC = No if it weren't for the explanations. Also:
You mean "one
of the most important things," right?

After the mandatory tutorial, the episode proper finally begins, and the player is greeted with the usual combination of grab-able SMB2 enemies (even the giant Shy Guys can be picked up). Not long afterward, the player comes across Bot sprite-swaps which, although they have playerblocktop=1, they cannot be picked up because...why can't they be picked up? It's unintuitive for a basic enemy in an SMB2 styled level not to be pick-up-able.
Something else to note: all of the world map levels say "Return to" or "Back to" whatever area. I find this quite in-concise since, in the episode's own canon, my character is already in said location. This isn't like ordinary SMBX episodes where I can walk from one level to another; I have no choice except to "return to" the area I just "left" (even though my character never really left in the first place). It would be better if you removed the "Return to"s and instead used various adjectives to describe the locations of each world map icon, even if it's something simple like "Perky Pastures (East)" or "Hushed Hollow (Depths)." Adding these minor details would also help to give your world more life (I think that's the right word).
Something that I'd like to point out:
Okay, so this NPC's sole purpose is to let the player know that collecting the all of the cherries in the section gives him/her a star...

So why does this NPC tell the player the exact same thing? I suggest removing the previous one (or at least changing what it says) since this NPC gives more details about the subject.

Some other things I'd like to point out:
This note block sprite-swap is on a layer moving horizontally, and that will cause Toad (and the other playable characters, I believe) to get stuck on top of it instead of bounce until the jump button is pressed. This is a minor issue, but I thought you should know about it.

Now this is something I don't understand: you have seemingly random player filters scattered throughout the early sections of Hushed Hollow (I know that you have reasons for the ones in some of the later sections). Even as foreshadowing for the later player filters, it doesn't really make much sense because the sections would only need minor, if any, adjustments to be completable as all characters. They just pointlessly break the flow of the episode more than anything.

Speaking of pointless, this part:

There are much better ways you could do the "foreshadow a later section" than warp chains. In fact, using a warp chain is probably the worst way you could have gone about doing that because the player is literally forced to go through multiple warps in a row just to get from one spot to another when one warp would have been much more streamlined; it was tedious when NSMGX did it, and it's still tedious here. What you did in Section 1 was better since the player is actually doing something on top of getting a glimpse at a part of the level further into the game. I recommend removing those little areas and move the gold pipe straight to Section 4.
Speaking of the first section, that key-wall part just seemed like a lazy attempt at recreating the key-wall segment(s?) in Super Mario Enigmatic; that part didn't really add anything to the level.
Behold, my first sequence break:
So, when I made it here, I realized that I could bounce on the rainbow shell sprite-swap to make it into the top pipe. At first, I was really exited because, since that's actually where the player is supposed to go and the sections are built that way, I thought that I had come across a legitimate split path and secret.

Of course, when I went back to see what was in the other pipe, I was met with a subcon, a Ninji, and a dead end. It was then that I realized that my sequence break didn't really accomplish anything.
By the way, Section 8 in the third level is practically useless; the Ninji can easily be moved to somewhere in Section 4 and the other part of the section is basically just another warp chain.
Not long after that, the player comes across the Garden Guardian, and there's something...familiar about it...
Wait a minute, this boss is just a rehash of D2 from Super Mario Enigmatic! LAME!!

Listen: it doesn't matter how popular your custom boss or previous episode was; rehashing a boss just comes across as being lazy. It seems like you had a bunch of good ideas, but then you got tired of working on the episode and just reused stuff from SME as filler.

So, at this point, I was just over halfway done with the episode, so I still thought that the episode might have a secret...
So I decided to phase through this wall, and I ended up stuck in that little decorative area and had to restart the game. As a level designer, you need to make sure that players can't get stuck to the point where they have to quit the game entirely; I recommend lowering the opening by one unit.

Speaking of decorations, some of them don't quite work properly:

Also, why do you have a pipe graphic here if it doesn't warp anywhere? It's not like the mushroom block needed any more indication than simply being there.

Moving on: this part is quite tedious:
In fact, it reminds me of something else that's tedious in a similar way...

AHA! I KNEW IT! Man, this has more in common with SME than I previously realized!

Another sequence break (I think):
In case you didn't know, if the player throws an item directly upward, then climbs a vine, grabs the item in mid-air and throws it up again, he/she can bring items up vines, like so. If you didn't intend for this to happen, you may want to change it.

Also, this guy should really be moved to Section 9 in Hushed Hollow because that's where the poison mushroom sprite-swaps first appear, and first time players probably won't realize that they're poison mushrooms until after getting hit. By having the message here, the warning is too late for first time players.

Something else you should know:
The text events for this dialogue don't paralyze the player, so I can jump around like this. Also, you mean "hero of
the Mushroom Kingdom," right?
Also, once the dialogue is completed, the chancellor isn't replaced by a duplicate NPC, so speaking to him again will trigger the entire dialogue again.

I have quite a few issues with this part. First of all, why can't the mini Shy Guys be picked up? Second, why aren't the mini Shy Guys used anywhere else in the episode (the Garden Guardian doesn't count)? Third, the first two mini Shy Guys are grey, so that means that first time players may mistake the mini purple Shy Guy's spiked helmet as just another grey Shy Guy and take an unfair hit (they are
mini Shy Guys, after all).

For this part, the Panzers are placed just high enough that they activate and begin throwing fireballs but the player can't see or react to them.
The only reason I got past them is because I was big and took a hit. I recommend lowering them down a few units.

And now, for something completely pointless:
Do I have to explain this? There's literally nothing for the player to do here except wait. The lack of hazards of any kind in this section just makes it boring, but the ship is moving too fast to make it feasible to avoid hazards if there were any there. I recommend either scrapping this section entirely or slowing the ship down and adding some hazards for the player to avoid.

This is also unintuitive:
Until this part, the player has to hit the switches as quickly as possible, but then suddenly, the player has to take his/her time and hit the switch at the right moment to proceed. First time players may not realize the sudden shift and end up taking an unfair hit.

Plus, for this boss, the buried rainbow shell sprite-swaps are set as a projectile generator, so whenever the player grabs one, he/she is launched into the air. Changing the generator to a warp should fix this.

Oh no, it's...it's...
I wrote:AAH! THAT NOISE! MAKE IT STOP! MAKE IT STOOOOP!

To be fair, this part isn't as bad as the ones in SME, but it's still annoying.
In this section, the pointless player filters strike again!
Seriously, why do this? The filters are so close together that it just becomes annoying having to switch between the different characters so frequently, and it's not like the areas that the players go through are built around said player characters (except the one after this section built for Peach).

Also, you have a Subcon here, but it doesn't say anything; it's just sorta there. Was that intended?

And now, I'm going to take a moment to complain about the most difficult part of the episode:
This freaking section...there are so many snakes and generators spawning at different rates (some snakes shoot bullets) that it's practically impossible to get past those parts without getting hit. If the player does manage to make it past all of that, he/she makes it here, where there's a Chase AI jumphurt=1 Para Shy Guy. Remember: Peach can't spin-jump, so she's defenseless against this foe; not only that, but I swear you built this part of the section around SMBX's Chase AI because it's practically, if not completely, impossible to get past this NPC without taking a hit. The only way I was able to get past this part of the episode was by bringing the snake pot with me to kill it, but that wasn't much easier to do. Not only is this a completely ridiculous difficulty spike in the episode, but it's so difficult that I was disappointed with The Grueling Grotto and even the final boss because they were just so much easier than this part. You really need to tone down the difficulty in this part if you want to keep a steady difficulty curve.

I knew this already, but I just wanted to let you know that you put the message a bit too late in the episode; you should move this guy to where the silent one is (in the previous section).

Moving on to the final level:
Although you have a message box appear when the event is triggered, it's triggered by an invisible ax, and the mask is too close for first time players to be able to avoid it.

Also, I recommend having two mushrooms here instead of one; it gets a bit tedious having to go to the world map then back into the level just for an extra mushroom.

Plus, that red S-Switch can be difficult to see with the HUD in the way. I recommend lowering it by one unit and changing the color.

Finally, although you had shell-riding sections before, you never had it so that the player had to short-hop to avoid running into walls, lest the shell would leave the player behind. I recommend adding a warning of some sort for first-time players.

And now, the final boss:
So, the final boss's grand strategy is to try to push me off the platform with blocks? Well, at least you tried to make something unique and original instead of resorting to using the editor's pre-programmed boss AI--

Oh, nevermind.

The events should hide the "Spawned NPCs" layer, because since they don't, I'm going to get killed no matter what I do.

The puzzle part right after that was well done, though.
Okay, this is the part where it gets to be a bit unintuitive. The dialogue does hint that I need to shell surf, but it also directly states that I need to destroy the vases, which are clearly right there.

Well, I threw the shell sprite-swap at the vase, hit it directly, then I tried to grab it again but I missed and it fell into the pit. Then I saw the vases change, and I realized that they weren't vulnerable until right then. You should add a better warning for first time players, or maybe not have the vases show up until after the Panzer platform has situated itself and the player is forced to shell surf.

Actually destroying the vases merely takes knowledge of what's going to happen as well as patience so you don't jump right into the mask. It's not that difficult.
Also, why did you have this statement in Drow? I don't know what you're referencing, and neither will plenty of other people.

Once again, the NPC isn't replaced with a duplicate, so talking to it again triggers the entire dialogue a second time.

I was also a bit disappointed that the other elders don't say anything; only the main one gets dialogue.

Maybe now that I'm back at the chancellor's room, they will say something--HOLY CRAP, I JUST KILLED TWO OF THE ELDERS! WHY DIDN'T YOU TELL ME THIS WOULD HAPPEN?? NOW ALL OF SUBCON IS DOOMED, AND IT'S ALL MY FAULT! Wait, maybe I'll be able to redeem myself in the sequel: "Mario Prime II: The Elder Stomper."

The rest of the ending was really well made; you managed to tie up all of the loose ends nicely, almost as though this were professional.
Before I conclude, I have something that needs to be said: your custom songs aren't labeled! Did you learn nothing from Super Mario Enigmatic? Come on: music is just as important to levels as graphics, especially when making cut-scenes. Where are your custom songs from?
IN CONCLUSION:
This episode parallels Super Mario Enigmatic quite a bit, and not just because this episode stole some of its design choices from it: both episodes are uniquely designed, and both episodes have some flaws in their execution. I wouldn't be surprised if this gets featured soon, but I do recommend that you at least change the Garden Guardian to something more original.