I agree there aren't many third-party characters left on the same level as Snake, Sonic, Pac-Man, Mega Man and Ryu.
That being said, I think an approach I'd be okay with for future third-party characters would be those heavily associated with Nintendo. I suppose there aren't as many examples nowadays other than maybe Phoenix Wright or Professor Layton, but there are so many memorable NES characters that would be really cool to see alongside some of the cast. Simon Belmont is probably the biggest one, but I wouldn't mind seeing Bubble Bobble, Ninja Gaiden, Contra, River City Ransom, or Double Dragon represented down the road. With Capcom involved I wouldn't mind seeing Ghosts 'n Goblins, Bionic Commando, or Final Fight involved at some point either.
Again, I'm not clamoring for any of these characters and I don't think any of them are very likely, I just think it'd be a cool approach to third-party characters in the future since there really aren't very many big names left.