Mega Man should be like good ol' Smash Bros. 64 where B and Side-B are the same! Then he could run around shooting like a maniac!
On a side note this could make for a very interesting gimmick where downed players drop a Large Weapons Energy item when they respawn. The item would drop and fall in a similar way to how Dragoon Pieces are dropped from downed players. Mega Man could grab it before it fades away in order to recieve a new weapon (a la Kirby). For instance, Mario and Bowser would give Mega Man "flame style" while Link/Marth/Ike bestows the Blue Bomber with "sword style".
To keep things fresh (and separate from Kirby) Mega's regular attacks would become more attuned to his current style as well. For instance that one-two punch combo would now have flaming fists, or it would be up-close attacks with Slash Claw.
Actually now that I think about it, Star Force MegaMan (aka Geo Stelar and Omega-Xis) would be better for a Smash Bros. game with the above gimmick. No matter how dorky Geo and his friends are, they DO have that whole "Noise Change" thing that they do in Star Force 3. All of the Noise Forms have differently-shaped armor, but without noise they're all blue and lite-blue like Geo's "normal" form. The armor shape is a great way to tell players what style they currently have equipped, and the colors can be swapped for different outfit schemes.
Plus it would be cool to have RED GAIA... ERASAAAAAAAA!! as a Final Smash
