I use Mega Man as well, so I'll weigh in.
Mewtwo may be light, but Mega Man really struggles to get the kill if he's not using an aerial since his options to do so are pretty laggy and somewhat predictable/hard read dependent. They also require you to be close to Mewtwo, and a good player isn't going to be close to you anticipating this. Meanwhile, Mewtwo can kill with his Shadow Ball fairly early if he hits Mega Man as he's experiencing lag. It also goes right through his pellets. Shadow Ball can also punish Mega Man at range if he has a bad landing since none of his aerials other than n-air autocancel. Leaf Shield doesn't defend from SB either. Overall, Mewtwo kills easier than Mega Man does, but he still has to watch out and know when to go in, as dying from an unexpected down smash or up tilt at 70% is a real risk.
Confusion doesn't do too much versus mega man except reflecting side smash as you said. Mega Man's side smash is essentially useless in this MU I feel. It can also reflect his side B and Metal Blade which don't have a ton of reward. You're better off trying to catch Metal Blade.
Disable can be good if Mega Man misses a hard read, but using it in neutral is tough because Mega Man's pellets outrange it. What I like to do is punish poorly spaced down tilts with it since they have enough landing lag to give you the opportunity to use it.
Mega Man doesn't have much pressure from afar, he excels more at mid range while Mewtwo is better at far range. This means Mewtwo can camp him out better than most other zoners.
In terms of neutral, it's up for debate who has a better one. Mega Man has his pellets and Mewtwo just has down tilt, jab, and shadow ball. Mega Man falls fast, which means landing is riskier. This could potentially lead into an up smash punish from Mewtwo.
Mewtwo falls pretty slowly. Mega Man can abuse this by using up air, which is a very effective tool against Mewtwo. Note that Confusion can mitigate this slightly, however.
Off stage, Mewtwo can gimp Mega Man's recovery pretty easily since it lacks a hitbox. Mega Man can't really gimp Mewtwo as easily, although his Leaf Shield can steal his second jump, which is extremely important for Mewtwo's recovery.
Mewtwo should stay on the ground in this match up, and Mega Man should use his aerials to his advantage, as Mewtwo doesn't have much defense against them.
For customs, Mega Man is going to want Danger Wrap over Crash Bomber. Mewtwo struggles to land, and Danger Wrap makes this even harder for Mewtwo to do. Skull Barrier can be used too as a reflector, but Mewtwo will always win the reflect war unless he's not prepared, so it's usually not worth it. Ice Slasher could potentially be interesting and put Mewtwo in a bad position in the air, but it's usually outdone by Danger Wrap. Don't use Beat.
As Mega Man, you should use: 1311, 1312, 1313, 1211, 1212, 1213. All should work fine depending on preference.
I say 55-45 Mega Man's favor. With Danger Wrap, possibly 60-40 Mega Man.
