You make a number of general points I largely agree with. I think you are overstating the likely naivete of the 3e designers.
Perhaps I am. However there are a number of other areas in the game's design where there are similar issues where the new mechanics completely change the balance of the game, particularly at high level (monsters getting ability score bonuses, fighters have to take a full-round action to make multiple attacks while casters can move-and-cast any standard action spell, the huge reduction in time required to prepare spells, the trivialization of spell interruption, cheap & easy access to wands/scrolls, a different saving throw structure where stat & spell level & caster level determine the difficulty and high-level warriors & monsters no longer have among the best saves in the game, multiclassing with caster levels).
It's been written that many of the core issues with 3.x didn't come up during the playtesting because the playtesters generally played the game as d20 AD&D, and thus many of the balance issues not coming to light until the game had been available for a couple of years. So that would indicate a certain naivete of the 3.x designers. I suspect that many of these issues took them as much by surprise as it did the rest of us. "Let's take AD&D but make the rules more logical and consistent, and let's get rid of some of those arbitrary restrictions and un-fun bits while we're at it."
I would say their effort here was quite successful in extending play into the higher levels, however they were under pressure to preserve the feel of these classic spells close to their the original text. To have even partially accomplished that feat was perhaps even evidence of the outright superiority of 3e to its predecessors.
They were successful in extending play into the higher levels, for better or worse. It seems like a lot of people don't actually like playing (or especially DMing) 3.x at high levels, although that's a gut feeling from reading message forums and not based on any actual data. I wouldn't say that it shows any "outright superiority." I would argue that BECMI D&D did a much better job of supporting play through high levels (36th) while remaining playable and retaining some measure of balance.
Someone on these forums -- my apologies but I can't remember who -- has frequently stated his belief that D&D is a 10-level game at its core, and I'm inclined to agree.
In hindsight, I would vehemently argue that half those spells should have been rewritten completely from scratch, for the reasons you stated. But at the time, such a choice would have been rated a strike against, evidence 3e was "not really D&D".
Rewriting them is one option, but yes, that could have gone into "not D&D territory."
Frankly, I think that the 7th-9th level spells should have been left for the Epic Level Handbook, as that would have matched their original concept much more closely (since by that level, 3e characters are no longer gaining a full level's worth of improvements). It was a huge mistake to start coming up with character abilities that are more epic than
wish, miracle, time stop, or
true resurrection. Those should represent the limits of mortal power, with everything else being scaled accordingly.
IMHO the majority of the 3.0 design problems stem from adhering too closely to the original material. 3.5 put a band-aid on a number of them, but I think it is Arcana Unearthed that shows us the real potential of a 3e-style system. It was easier for Monte because there were no expectations other than fun.
Agreed on adhering too closely to the original material. I don't know that straying from the original material in order to make a better-designed game was the answer, as that's very much what 4e did, and we see how divisive that was (I recognize 4e as a well-designed game, but I don't really like playing it). That original material is a big part of what gives D&D its identity.