There is an easy way to do this with BESM d20: Drop the classes entirely. Each time they level up, characters get 10 Character Points to spend, and they have to buy HD, BAB, Saves, Feats, Skills, etc. with those points per the costs listed in the book.
The BESM d20 system was specifically designed to do this; Guardians of Order ensured that all classes ('cept one, but it's a special case) in the book add up to 200 pts. at 20th level.
Check out their free "Anime d20" SRD online if that's piqued your curiosity any!