Or they could complete that weird Duo storyline with the evil energy.
That could be a fun tangent to go off on. We really don't get a lot of explanation for some of the alien stuff in the games, proper. The Stardroids, Ra Moon, the Evil Energy...the Archie comics and the Megamix/Gigamix manga actually gave us more explanation than ANY of the games did.
Actually, I'm not sure it would. You basically want to take a beloved by fans hero character and make him a bad guy. It MIGHT be interesting, but I imagine more people would whine about it. Of course I'm not sure if X being the bad guy in the Zero series had any fallout either. I also can't remember if they established it was Copy-X from the get go either.
I CAN say that another issue I have is simply the fact that not having Wily be the villain feels wrong. It works for a game here and there. (MegaMan V for the gameboy) But just ditching Wily? That'd be like the next five Mario mainline games don't have Bowser as the big bad. It just doesn't feel right.
Well, Zero being evil in the past is a pretty well established part of his backstory at this point. This would be less "Hal Jordan becoming Parallax" and more "Wolverine back when he was brainwashed as Weapon X". Plus, we don't even know HOW Zero was originally. Was he always a berserker? Was a copy of Wily's mind in control? Was he even ever awake in the Classic Era, or was he basically just sealed away like X right away? There's a few ways they could go with it.
As for Copy-X, I think they revealed it wasn't the "real" X by the end of the first game. So, people didn't really have any time to get TOO mad about it. I think there WOULD have been, though. But, that's a different set of circumstances. That would be tarnishing a hero's legacy. Exploring Zero in the Classic Era would be more about explaining and expanding the history and connections with the franchise. As long as Zero doesn't kill Roll or the animals like Rush or Tango...I think fans would be okay with it. Protoman would be a fair target, though, in my eyes. He's been slowly walking towards his "heroic sacrifice" moment in the sunset for 30 years now. Maybe even Dr Light, since we still have hologram-Light waiting in the wings.
As for Wily being pushed to the side...well, we know from Gameboy Mega Man II that Wily eventually reforms (...then his past self convinces him to steal and modify Rock into Quint and make a copy at the same time creating Rockman Shadow, eventually leading Mega Man to possibly kill his own future self by Gameboy V...do you remember what I said about the timeline being wonky?). Maybe Wily could be a ally in the games where Zero is the villain, making upgrades with Auto. It's not perfect, and we've seen that before, but he could still show up. Or maybe Mega Man needs to save Wily FROM Zero, which would be a interesting inversion.
It doesn't really BOTHER me to have Wily as the main villain. But, it's not really INTERESTING, either. It's just part of the formula, at this point. Honestly, the only way to make Wily interesting is probably to have him be forced into subservience or working alongside some other villain. Kind of like the Eggman/Wily team up in the Archie Comics. It was actually interesting to see that Wily had lines he wouldn't be willing to cross. You could do something like that in the games.
