I kept playing and reached the final stages of MM5 by beating Gyro Man and Crystal Man.

Crystal Man's stage was annoying because you have to jump over spikes while avoiding falling crystals. If they hit you during a jump, you basically have no chance to recover. Other than that, the stage wasn't too hard. I mostly fought Crystal Man with MM's standard weapon, but I hit him a little with some of the other stuff. He had a pretty simple pattern of jumping and shooting.

Gyro Man's stage was tough to master, but now that I'm used to it, it's not bad to get through. Gryo Man was weak to a gravity weapon I have, so I took away 2/3 of his health with that, and hit him with charged shots for the rest.

So I'm starting the end-game stages, which seem tough. I'm waiting to see how long it takes before Wily is revealed to be the true boss. I'm sure it'll happen. But so far, the game's still sticking with the Proto Man story.