Super Smash Flash 2.

[Gaia]

Also there seems to be a consistant issue with each character's respective art style (Project X Zone found a way around this, so you should look into that, I am doing something similar too with my current sprite project).

Which issue are you referring to?

Style clashing, which is has been pointed out before.

Also there seems to be looping issues with the music as wel,

Which songs are you having loop issues with? I believe there's only one that's completely botched and we've already squashed it in v0.9.

It's the menu theme that has a bit of a delay before the song starts up again after it finishes.

(with the ever oh-so controversial) Mega Man's weapon ability seems very akward to properly utilize (I'm having to hold down one of the wsad keys while selecting a weapon? how does this work? It also leaves the player vunerable.)

We've gone through quite a few revisions of this move, actually. Generally feedback on this one has been the best, especially from competitive players which were asking for a quicker way to get the power they wanted.
What you do is, hit down+special and hold special as you hold a direction (or no direction for mega buster) and release special. Sounds really complicated, but it's the best way to do on-the-fly switches quickly. If you hold downB you should get a feel for which power is where easily.

It can get complicated with four Mega Men running around on the feild, but I suggest keeping down+special with metal blade, hard knuckle as foward+special and beat as up+special. back+special should be proto-strike (the sheild) by simply hitting those comands rather than holding downB which would slow the fight down.

But I'm glad you are handling this well though.