Basically, I find it rather frustrating that someone who TRs with, say, a +3 Dex tome, still has to read a +1 Int tome at level 3 if they want TWF before level 7. Or that a wizard who wants more DC and skill point while they level has to read a +1 Int, +2 Int and +3 Int tome before reading their +4 Int tome at level 14, or needs to Lesser Reincarnate just to fill in the back benefits.
My suggestion, then, is to remove the ML on tomes, but to have them apply their bonuses upon being read in the same way that the tomes unload when you LR. That is, you can read that +4 tome at level 1, but it won't give you any benefit until level 3, when it will grant you a +1 bonus, a +2 at 7, etc...