Atomic Planet didn't emulate the NES games.
Back in the PSX days, Capcom decided to rip people off (in Japan) by porting the 6 NES Megaman games to the PSX as sold-seperately PSX games. They tossed in the remixed MIDI versions of classic tunes that were made for the arcade games, and bloated them from MIDI to pure CD audio because... they might play smoother or something. I dunno. Capcom didn't give a crap about space, because they had entire CDs to waste on several-kilobyte NES games.
Combined with the inferior PSX version of Megaman 8, Atomic Planet ported 7 PSX games to the PS2/GameCube, which was apparently easier than porting 6 NES and 1 Saturn.
The PS2 happened to be able to fit 7 CDs on one DVD. The GameCube couldn't, so Atomic Planet decided to start slashing features.
Messing up the buttons was just inexcusable. Especially considering that the PSX versions that they ported all had "button config" settings in their options menus.