Most of the changes are cosmetic (and very cute, may I add, love that Roll!). I think some of the later games edit Robot Master palettes to look closer to their official artwork. There's some sprites in Zynk's thread on this game that demonstrate a potential makeover for Crystal Man.
Out of curiosity: Are these hacks compatible with other Mega Man/Rockman hacks, like No Constancy, 4 Minus Infinity, or Burst Chaser (or, once 5 is released, Air Sliding and things like Wily's Dream Space)?