Why not make racial bonuses just start with some bonus points in certain CP categories.
For instance High Elf starts with Tier 3 magicka bonus and maybe one of the random passives such as the AoE oblivion one. That way early on its a nice bonus for your gameplay type, but end game it really has no effect.
While Khajit can start with tier 1 stam tier 1 magicka and maybe pickpocket rarity increase passive. Etc ETc.