Nintendo ALWAYS used their trademark characters for all their games. If it didnt have a trademark character, then it wouldn't feel like nintendo.
The FFVII exploit is one thing, because their RPGs are always about telling elaborate and unique stories, but with nintendo's party games, that doesn't really matter.

It sounds to me like your complaint isn't so much about an overuse of mario's character, but rather an underuse of him in the single player adventures that we've all known him for.