Spin-off game, you say?
Revolver Ocelot. Set between MGS 1 & 2, it could have a sort of Jekyll & Hyde theme to it, trying to keep Liquid from taking control.
I agree about Chrono Cross. Waayyy too many characters to keep logical track of. I recall something similar in Chrono Trigger with Magus. He didn't have many lines once he joined the party... I guess because he was optional.
I think Zero from the Mega Man X series could benefit from some more backstory. Granted, X4 was the last I played, and I think they're up to X7, so maybe that's been covered and I missed it.