If I remember, Sonic Battle. You put points into Emerl for customization for moves. Then, there's Dragonball Z Budokai, the series. Other than that there's also Sonic Chronicles, however, I find it a little broken on this one, once your main 'hog Levels up, everyone else does during party organization, broken I say. =/
Well, Super Robot Wars or any other tactical game lets you customize your units, say Advance Wars and Fire Emblem. Don't forget in Shin Megami Tensei's Pokemon Knockoff, DemiKids, you can customize yer demon, as well as other breeders.
RPGs pretty much let you use points for characters, anyway. Then there's sports and such, but I won't get into details there. Some fighters do let you customize your fighter, as stated. Oh, there's Sigma Star Saga, if anyone remembers that title.