I decided to chuck all of that and build a system that seems fair regardless of how the wizard chose to play his character and that was consistent for all spells the wizard gets. As I mentioned before, I haven't had anyone play a wizard yet (it's only our first 3E campaign) but my players have made it clear that it isn't because they think my rules are too hard or too easy. I would still want to see my house rules playtested before I recommend them too highly, but if they don't work for some reason, I think I'd try to tweak them rather than go back to the rules given in the PH.
From previous conversations on this topic, I know that a lot of other people are not as bothered about this consistency issue as I am. I guess we all have our little peeves about the system.