Yeah, same problems there. The same synth brass patch on everything, bar the bass. And the PSG squares are just tasked with playing chords over and over. The arrangement is the same.
I made this Genesis-style remix of Sonic Advance 2 a year ago:
http://www.youtube.com/watch?v=c-pRIxhXm-4
PSG channels are constantly switching between being used for chord progressions (I looked at Green Grove from Sonic 3D for some ideas there), backing the lead melody or playing arpeggios. By having the channels switch tasks every once in a while you make sure things are kept interesting and varied, which is a common trick for chiptune arrangements in general. Synth brass plays the normal full note chords, a glockenspiel-like sound for lead melody which is filled out by the PSG, etc etc.