I wasn't really clear, let me explain!
The music : GBA's music chip is inferior to SNES', so every sound effects/music sounds crappier.
The controls : I noticed several things, ie. not being able to control up and down underwater or with the animals. The physics are pretty much all redone.
Too bright : Problem with gba was no backlight (fixed with DS) so they made every color brighter to make it visible.
Less visibility : It actually looks alright when I look at it now. But with FF6 the screen was cropped. Snes and Gba don't have the same resolution and screen size. Everything would be really small if it was just a port, and imagine the same text size as gba on a tv.
That's pretty much what I meant! Compare those video to see it yourself :Toxic Tower GBA
, Toxic Tower SNES
Listen to both musics and sounds, watch how stuff move (different physics). I think they made it all green on GBA to give a water reflect effect with the acid so I can't blame that. But still.
Maybe I'm just really picky, everyone is like this with something he likes a lot