Well, it sounds interesting, I've never heard of "Mega Man Powered Up", but it should be neat. As for which game to use, there are a lot of factors and I don't know the series very well, so I can't recommend specifics, but I can tell you how I'd go about deciding. The primary factor should proably be ease of hacking.

The first thing you should consider is which game is closest to your end goal so that you can avoid reimplimenting anything you don't have to. So, perhaps the game with the largest feature set could be the best choice. However, sometimes the most featureful version of an engine has so much stuff crammed into it that it can be difficult to alter.

Ultimately, it really depends on the game's internals. It also depends on your goals. If you're interested in reverse enginering, documentation or utilities don't matter much. However, if you're simply interested in getting to the end goal, perhaps the proper choice is the game that's been researched the most extensively.

It may be helpful to try and get in touch with the authors of other Mega Man hacks and ask what they think of the various game's internals and hackability (or lack thereof). Sometimes a series of games share a substantial amount of the codebase and they aren't that different, so the choice doesn't matter much. But other times, they aren't really related and it can make a big difference.

If you've got lots of patience (and a bit of insanity), you could take a look at each of the games and do an in depth comparison to see which matches up with your goals the most. This could be fairly easy if they are well documented and you can just compare them without much work. However, if you're going to have to research your target personally, it's probably not worth the effort.

Sorry to ramble on for so long and not actually give you an answer, but hopefully I've given you some things to think about.