As a fix for current 3.x games, I can see a polished up version of this working quite well. However, given the assumption that we're going with the level of overhaul implied in a change of edition, I'd just as soon they tossed all the boring buff spells (flat stat buffs, AC buffs, hit/damage buffs, or any other buff with only a numerical character sheet effect) out the window and re-adjusted mid-to-high level encounters to not require all that prep time and accounting. I sort of disagree with Hussar. Yes, a party that does not spend all its time buffing before combat has substantially more spell-resources at their disposal during the encounter. Unfortunately, as Gold Roger points out, even if the buff spells are slightly weaker than their fellow spells at any given level (and you'd have to make a pretty good arguement to convince me that's true), they make up for the lack by having dumped a lot of their resources outside the 1 standard action/round portion of combat. If one casting of bull's strength is about as effective at depleting enemy resources and/or protecting your own resources as scorching ray, hideos laughter, or summon monster II then the buff is the better option because it's casting time amounts to a swift action. Since save DCs are based mostly on spell level, this becomes even more exacerbated in high-level play because any low-level spell that requires a saving throw is less and less likely to succeed at higher levels, while beneficial spells cast on friendly targets never face this hurdle. Buffs just become the only really useful expenditure of those low-level slots. Make stat-boosting just be a more integral part of leveling (I figure if I spent most of my time swinging a sword, dodging fireballs, and getting beat near-to-death, I'd get stronger, more agile, and physically resiliant a little more often than once every 12 levels) and add in a "last ditch effort" mechanism for short-duration power-buffs, like action points. This would alleve the need for stat boosting spells and items.
Movement or environment buffs should remain roughly as they are, though. Getting a +5 to strength is boring. "Okay, Joe, you're a little stronger." Getting to fly or breathe underwater is more flavorful because it's something you can't usually do, not a slight boost to something you're already doing. The same would be true for invisibility, etc.
As for destroying Transmutation, I doubt it. There's so much that could have been done with that school that wasn't (at least in the core rules, since I don't have the $$$ to buy all these expansion books). The buff spells strike me as mostly lazy filler for a school that should have been much more flavorful.