I'm not sure I understand this. Why isn't this possible, exactly? Companies release open betas all of the time, so that players can present problems and have the developers fix them before the game is on the shelves. Even if this isn't a retail game, what makes this one any different?
Imposing the limits after the fact wont work out well at all. The game needs to be designed with these in mind to begin with. Even the way things are already, there would actually be a fair amount of redesign and refitting involved.
The point being, there's not much of a reason to sustain a notably large amount of effort on something so specific as stray colors. Sure, the kind of people who play Mega Man Unlimited will be much more centralized than the kind of people playing 9 or 10, but most of the players will not notice the faults in the coloring, some will notice them and probably not care, and only a select few will actually be bothered by them.
Megaman 10 at least makes it believable. And no, both 9 and 10 actually have rare moments of graphical infeasibility on NES hardware. The point I made is that this project isn't even close to believable in many instances.