As a Greninja player myself, I fail to see how interrupting his specials makes this a positive MU. Aside from Water Shurikens (fully charged ones can eat through every projectile but Leaf Shield to counter-poke, punish landings, and combo into his Fair) and a little bit of Hydro Pump. His other two specials are mostly situational and aren't even part of his core gameplan to begin with, so he really shouldn't be using them much in the first place. Yes, Greninja is a fast faller, but so is Mega Man, and Mega Man is not only a fast faller, but he's a heavyweight character too and is vulnerable to getting combo'd moreso than most. And do you like combos? Cos I do, and especially compared to Mega Man, Greninja's combo game is AWESOME. I'm even inclined to say he has some of the better combos of anyone in the game, at least top 10 in terms of comboing alone.
Nair > Fsmash/Jab
Nair >Dtilt > Dash Grab, Uthrow > Uair
Dash Attack > Fair, sometimes Uair can work too
Nair > Usmash
Uthrow > Uair
Uair spike > Dsmash/Fsmash (if you read it, you can tech it though)
Charged WS > Fair
Dtilt > Usmash
Utilt > Usmash/Uair/Bair, Utilt > Uair being a kill setup even
Dthrow > Fair (its a kill combo now as of this recent patch and a true combo at that)
Certainly more damaging than anything Mega Man can do. In addition to that his approaching moveset isn't the best but he has the mobility to get around lemons and his Fair and Nair (the latter being safe on block if spaced, the former comboing into a lot of things on hit). Lemons do harass him but he has ways around them, and he's got the edge when it comes to KOing with more kill setups and good baits for air dodging. Really, I don't see this being a bad matchup for him: Enough speed to manuever around your projectiles, decent kill moves, a projectile that can counter attack yours, and deals a more damage than Mega Man in general. As a co-main of both characters
, I honestly feel that this is a mostly even MU but I'm actually gonna call it 45:55, Greninja's favor. If you're fighting Greninja's who are over-reliant on specials, you're probably playing bad Greninjas. You do win the neutral game, but when it comes to punishing you have to do A LOT to keep up with him damage-wise.