I'm probably going to track down one of those retro controller adapters so I can use my SNES controller on the Gamecube. [to play Megaman Anniversary Collection]
I hate to be the barrier of bad news, but this won't solve the problem. Even with a SNES RetroPort, the SNES B button will STILL be mapped to jump and the SNES A will STILL be mapped to fire. This can be adapted to, but it would literally be as bad as a controller that put the dpad on the right and the buttons on the left. It would cause endless amounts of unnecessary frustration.
For this reason, I strongly suggest you play through the PS2 version if you want to casually experience the original Megaman games - NOT the Gamecube version.
The ONLY work around for the GameCube control issue is to either padhack a controller to permanently and deliberately reverse this (thus making it into a "Megaman Anniversary Collection only controller" or go with a rare and awful third party GameCube controllersthat allow you to reprogram button layouts on your own. The issue here is such third party controllers aren't even worth bothering due to the decrease in quality. As well, keep in mind the GameCube version completely lacks the Rockman Complete Works Arranged tracks, one of the major selling points of the original PS1 ports. The music from Megaman 8 was also downsampled, and starts at around 5-10 seconds INTO the tracks, not right at 0:00 where the tracks should start! It's really really weird. The game cut a lot of corners to fit on the GameCube mini dvd.
As much as I want to yell at Capcom endlessly for the GC build of AC, it's actually not really their fault.
Megaman Anniversary Collection was farmed out to Atomic Planet, who were tasked with porting the Rockman Complete Works over to the PS2 and concurrently, GameCube.
It seems Atomic Planet put all their eggs into the PS2 basket, as the PS2 build of AC is vastly superior to the GameCube version, including the same control schemes as were used in the Japanese only PS1 Rockman Complete Works set, including all of the wonderful Rockman Complete Works Arrangements, and including some nifty extras.
That said, the PS2 version does suffer from a handful of annoying issues. For whatever reason, the emulation of the NES titles isn't particularily vivid, even over component cables. The colors are washed out in comparison to their NES counterparts, and the contrast is too high. This isn't the case with either the GameCube or Xbox builds. The other problem with the PS2 version is that although all Rockman Complete Works Arranged tracks are present, they were placed into the game at too high a volume level. This means when you actually turn up your tv or surround sound speaker volume, you'll hear distortion!
The Xbox build came out a year later, and combines the best qualities of the GameCube and PS2 versions with having the best visual clarity, no audio problems in the arranged tracks, multiple control configurations and all of the bonus content that was split between the PS2 and GameCube builds. However, it too has it's problems - there are very odd emulation issues whenever in-game text is displayed. Although it does work on the Xbox 360, Megaman's sprite in Megaman 8 is extremely glitchy, missing several frames and making the game a mess to look at.
The good news is that Capcom has been releasing the original PS1 Rockman Complete Works on PSN for $5.99 each. Although yes, they'll be in Japanese, they are what Megaman Anniversary Collection should have been, had they been handled correctly. In particular Rockman 4, 5 and 6 Complete Works are very much worth tracking down for fans of these games.