Basically the instruments the game uses, changing the way the music sounds. See this port of a song from SMRPG to SMW: http://youtu.be/FDS6KFDjk0o
See how it uses SMW's tropical sounding instruments on the same song?
I don't have any experience with this but I suggest it's just loading a midi of this and then putting a SML2 soundfont over it.
Also since it's 16Bit and SML2's music is 8Bit I'd recommend making SML2 music with SMB3 or whatever soundfont so it fits SMBX.
Also if you really wanna make it SML2 styled then you should reduce the number of channels to 3 (?) since the GB had a max of 3 tones played at the same time iirc. I might be wrong though.