They did, that's one of the reasons why they included Bean and Bark in Fighters Megamix, but not Sonic & Co. Even though Bean wasn't a purely original creation (he was adapted from Dynamite Dux), those were still "their" characters.
Shinobi said:
It would've looked like primitive garbage on the Saturn anyway. :lol
It likely would've just turned out like VF2/FV with 2D parallax backgrounds. Amy's stage would've been redesigned to be stationary like Shun Di's in VF2.