Disclaimer I have no professional training in game balance nor am I a particularly high level player at the moment.
I think the main issue of mega man is an imbalance in his playstyle. Mega man's design seems to be that he is a very safe character with a relatively low damage output but is able to somewhat mitigate this with some burst damage conversions and clever projectile and item play. His flaw is supposed to be that he struggles at killing, most of his strong moves have either high cool down or startup, and while he does have some kill confirms that have not yet been fully implemented into his game plan, they are not particularly easy to do consistently.
My issue for mega man is that his safety and killing issue do not seem totally in balance. Mega man should have trouble with character who can penetrate his defenses, but in the case of sheik he worse match up, it is especially annoying that she is in general safer, has a higher damage output due to having very reliable combos, and has an easier time killing in general.
Safety.
Mega man's forward air does not due very much damage, is not super fast, and does not have good landing lag. Some part of this should be touched. Due to what I believe his design philosophy to be, landing lag would be the most likely target for a reduction. I personally feel that making this move come out on frame 7 instead of 9 would also not be a bad change either.
Damage
We all know that mega man's smashes are a little lack luster. Fsmash and Dsmash are the offenders here.
Fsmash
I believe that this move should have much less startup and maybe the projectile should move faster. The endlag should remain the same. Fsmash is not a particularly powerful move, but it is really annoying when someone whiffs a smash attack, and its faster to run up and upsmash rather that attempt to fsmash them. By reducing the startup, this move may be usable in certain setups as well as useful as a surprise attack, pivot fsmash anybody? With the end lag intact, however, if you whiff this move or they predict and powershield, you will still get punished for it.
DSmash
This move in my opinion should just be re purposed. At the moment its strong but slow, frame 17 for the strong hitbox, and way to laggy to throw out in most situations. Worst of all, however, is that it kills off the top. Up Smash and Up Tilt do that already. I think this move should come out earlier, but instead of being a early kill move it should be a damage dealer with little knock back growth. I believe that early demos have this move being a multi hit that lasts the entire animation, that's what I would make this move do.
Those are the biggest things I think would be good quality of life changes that wouldn't upset his design much. I didn't add anything that would help his disadvantage state much because I think Mega is supposed to be punished for letting someone get in on him, and I think our landing mix ups are reasonable.
Buffs that I think would just be cool. Dair auto cancels out of a rising full hop, acting out of neutral special faster, acting out of up special faster.