I love X more as a character than basic Mega Man, but they cover a lot of the same territory. The only thing that really separates the original X games (like X-X3...X4 onward started to get...different) was the Armor Upgrades for X; the basic premise and gameplay was otherwise identical (2-D side scrolling platformer Shooter hybrid; absorb boss powers to add to your arsenal).
I mean, I suppose the character could differ in that he would be faster thanks to Dash; be a Heavy thanks to the Armor and...what else? His most common upgrades were the dash (and Air Dash), Helmet, and upgraded Blaster. They could make him another 'meter' character like Hero with his Mp or Joker with his Rebel Gauge; where a Charged X meter allowed him to use more destructive Energy & Specials attacks. Still though, his base kit would still be firing lemons, charged blasts, and an array of his enemies' attacks.
Again, I prefer X because I like those games more, and they could differentiate him if they wanted to, but I feel like its already covered with Mega Man. Protoman would be a step down (he doesn't absorb powers; he just has a shield) and Zero, while a decent choice, would give us another sword user who honestly wouldn't differ too much from the others (quick combo'ed sword slices and occasional energy shots).
Bass & Treble as a Duo would work, I guess. They even combined in Mega Man 8, so you've got a decent Final Smash idea with that. He's got a few other types of beams than generic charged shots and can have Treble assist, but without the 'using your enemies moves' mechanic, he'd likely come off as a less versatile Mega Man.
I can't speak to Megaman.exe (heard the games were good), but despite being a grid based RPG, aren't the mechanics basically the same? Fire shots, defeat enemies, absorb their powers? His Kit would likely be similar to original Mega Man's as well. Disregarding Simon, I don't think they're going to give us another 3rd party character who's an Echo or Semi-Clone of one they've given us already. They've differentiated every DLC character (including Piranha Plant) fantastically so far.