Here's a general idea that I probably wouldn't execute by myself, but at any rate it's a concept that I've had in mind for a while.
Basically, my idea is a game that follows Proto Man's backstory and involvement in the story of Mega Man 3. Granted that MM3 in particular suffers from almost not having an explicit story, it always bothered me that the Mega Man games in general didn't do much to give a thorough backstory to Proto Man's character, it always had to be expanded upon by the series' related works. So this fan game would be an effort to shed some light on that backstory.
The game's story, explained in cut scenes, would be narrated by Proto Man himself. The game's intro would detail why Proto Man ran away from Light Labs, what he was doing in the interim period between MM1 and MM2, and how he came to find Dr. Wily. Wily is able to temporarily repair Proto Man's unstable nuclear core, gives him the Proto Shield to compensate for his weakness, and disguises him with his trademark helmet and visor. Thus begins Proto Man's employment under Wily.
Then begins the story of Mega Man 3, and the opening cutscene for this game. On the surface, Dr. Light and Dr. Wily have joined forces to develop a peace-keeping robot called Gamma, and Mega Man is tasked to go collect eight energy elements after the MM3 Robot Masters meant to go mine and retrieve them had suddenly gone haywire. To hide Proto Man from Dr. Light, Wily begins meeting with Proto Man in secret, and lets him know that his new companionship with Dr. Light is a ruse, and he is responsible for the defiance of the Robot Masters. With this, he asks Proto Man to retrieve the weapon data and Robot Master chips from the Robot Masters Mega Man destroyed. He also commissions Proto Man that, if he should encounter Mega Man, to destroy him. In exchange for agreeing to do this, Wily gives Proto Man the Break Man helmet and the Copy Ability, and he would receive a rebuffed version of a given MM3 Robot Master's weapon after each chip collected. At this point you're thrown into the main game, and each stage is a MM3 robot master stage, redesigned so that it feels fresh. Each Robot Master chip wouldn't be guarded by another Robot Master, per se, but perhaps a boss like a Mega Man game's Wily Stage boss.
After retrieving all the chips, Proto Man encounters Mega Man under the guise of Break Man. At some point during the fight, Break Man would reveal himself to Mega Man, and Mega Man would thereupon try to convince him that he's choosing the wrong path. Proto Man defies this, but after the fight, Proto Man reconsiders and independently decides he's going to help Mega Man by helping him in secret to infiltrate Wily's Castle. The subsequent stages would be the Wily Stages, leading to Proto Man witnessing Mega Man defeat Gamma, and rescues him from the Castle's collapse, returning him to Dr. Light's doorstep.
The closing cutscene would be a continued narration from Proto Man, explaining why he chose to fight for the greater good, how he learned to forgive Dr. Light, and how he decided that from then on, he'd make his own legacy. Then there would be a montage of Proto Man's appearances in later Mega Man games, through to Mega Man 10.
Really, this is as far as I've developed this idea. I think it's an air-tight concept, but I wouldn't go about executing it myself; it just seems to me like a lot of work to go about turning it into a fan game. So I leave it to the rest of you to decide what to do with this idea, and possibly consider turning it into a fan game. If anyone does do so, I'd be happy to work on some sprites for it.
Some additional ideas for this game that would be set apart from the game's concept:
-An easter egg of sorts: The player can find a secret passage in one of the levels, and find a pickup that is supposed to represent Bassnium, but is never named as such. In exchange for finding this pickup, Wily gives Proto Man an adaptor to his Proto Buster that can rapid fire, much like the Bass Buster.
-Though the bosses aren't going to be Robot Masters per se, as explained in OP, I would suggest opening up a contest for best boss designs among the forums, and the winning designs go into the final game, much like what Capcom did for the original Mega Man games.
-One of the problems I had with Mega Man Rock Force was that I felt the stage gimmicks got in the way too much of pure gameplay. New gimmicks and new graphics are fine in the case of this game, but it should not be trying so hard to be different that it doesn't feel like the game it was inspired from.
Might add to this post some more if any more ideas come to mind.