Ugh. Please don't bring up Atomic Planet. There's a huge thread I started way back in June that you can find.
Basically it comes down to AP being retarded and/or lazy. I'm sorry, but there's no excuse for using the PS1 works collection as a base. Unless the excuse is that they're lazy. But instead they blame the media format instead of their own programming. So the guys behind Mikami can make Resident Evil 4 (either disc, you pick) look that good with audio and what not but they have a hard time putting 6 NES games, 1 SNES game, 1 PSX game, and two arcade games on one disc? Sorry, I don't buy that.
The excuse that the PS1 works collection had the weapon swapping and what not is just a bad argument, considering the horrible control scheme for the GCN version. It's like their QA people (if they even have any) didn't even bother playing it before going gold. What's the point of being able to switch weapons when you can't even fire/jump correctly? In that case I would've rather just had straight emulation with all the slowdown.
Plus the MM7 ending has parts of it left out. Couldn't code part of the Mode 7 or something? Again, laziness.
Not to mention the WORST menu selection for a collection yet. Gee, why not have the main menu be a standard Mega Man stage select screen with the title shot of every Mega Man number, and then you can press R or L to get to the Options menu (that lacks a controller configuration) and the extra unlockables. But hey, what do I know?
Sonic Mega Collection, Legend of Zelda Collector's Edition, etc. were all done better, with the exception of Majora's Mask, but Nintendo had the guts to be honest and tell the user up front about some glitching that might occur.
Edit:
How is the GCN layout defensible? If anything, JUMPING is the main button you press during Mega Man games. You'll be pressing that a whole lot more than you will shooting if you're even somewhat proficient at the Mega Man games, even moreso in the later games where the jump button also is used for sliding. At the very
least there's no excuse for them not to even have a configuration. And as for Gamecube owners being 'lucky' that it was released on the system? Mega Man has more roots with Nintendo than Sony. And considering the GCN version outsold the PS2, I think it's lucky that PS2 owners got it. A much larger install base to sell to and it gets outsold? There's no excuse for it like Link being a playable character in SC2.
Sorry for the rant, but MMAC is just one of those things that should've been done right the first time.