For Megaman on the
NES, "A" was "jump" and "B" was "shoot" (as it was with just about every other good side-scroller).
For the
SNES, Nintendo (thinking they knew everything about videogame controls) put A & B on an angle, but Capcom (and just about every other good 2D game maker) decided that was the
wrong angle, so they made "B" jump and "Y" shoot. They also usually included button configuration options, for people who disagreed.
On the PlayStation, Capcom used the exact same controls, except that they used Sony names for the buttons.
When Nintendo made the
GameCube controller, they moved the X & Y buttons, for no apparent reason. But they kept the slanted A & B.
People making PS2-to-GameCube controller adaptors noticed that if you were to pull the "A" button down a little, and move the "B" button up a little, you would get the four-button diamond pattern that the SNES and PSX used. So that's what most of them did (a few of them supposedly shifted the X & Y buttons back into their original positions).
Atomic Planet ported the PlayStation versions of MM1-8 to the PS2/Cube (which is why they couldn't all fit, and had to have extra features slashed from the GameCube version).
They noticed that the GameCube controller wasn't the same as the PSX controller, so they invented their own control scheme, without looking at Megaman/Capcom history (or just about any 2D games), and made "A" shoot and "B" jump.
Heck, even "Megaman: Network Transmission" on the GameCube used "A" jump and "B" shoot.
Atomic Planet's controls are entirely backwards from the NES control version.
Had they done "A" jump and "B" shoot, MMAC would've sported "NES style" controls (with that improper slant, which Nintendo is fond of), and not only that, but just about any PS2-to-GCN controller adaptor would've converted it into "SNES and PSX style" controls.
And then to top it all off, Atomic Planet failed to include the button config options that were in the PSX games that they were porting from, which could have solved everything.