I'm not sure that the difference in spell school is a mistake. Say, for example, that abjuration handles Stoneskin. That's fine and dandy, but in order to get Greater Stoneskin, it's an entirely different principle of magic to work on; while abjuration allows a cover of stone to be created over yourself, Greater Stoneskin requires that you actually transmute your body to a degree. As well, while Haste is transmutation, the stronger variant needs to call upon enchantment to induce speed in an entire group.
I rather like the variety, and I think we all know there are other illogical things that haven't been changed, or changed yet.