Sorry if I am making suggestions too fast, but I think these ones will make much more sense than my previous one.
Diddy Kong
Why not put DK's favorite nephew Diddy Kong as playable in the game? The "fighter mini wiki" at SSBC states DK is rarely seen without his best friend and nephew Diddy.
Dr. Neo Cortex
Maybe not in 0.9, but expanding CB universe's characters in 0.9.2-1.0 would be a good idea, since Crash will be in 0.9.
Toon Link as Link variation
I think that Toon Link must be a variation of Link instead of his own character. Even at 0.9, Ken will be just a variation of Ryu.
Bass/Dr. Willy/X/Zero/Axl
One of those could be the 2nd character in the MegaMan universe of SSBC.
Servine/Serperior
Just thought that Snivy needs a heavier alternative.