Besides some of the multiclassing issues (I don't think at least 3.5 ever really solved the problem of making arcane multiclasses that didn't either dilute your spellcasting too much or alternatively make you question why you would ever play a pure spellcaster) I found that at about 14th level the GMing overhead on using a lot of the opponents you needed to to make a proper challenge was more than I felt like dealing with.
(Unlike the e6 crew) I think the sweet spot for 3.x is level 7 or 8 to 13 or so, 14 I consider near the end of the campaign. I am inclined to agree the combat can be harder to set up then.
even if there's nothing quite serving your purposes out there, chances are if you're adding in more than about 20 pages of houserules, there's probably something closer than what you're currently using.

There are few games Ive tried that I would run again with that little in the way of houserules, besides GURPS, and each of them I would only use for their specific usecase. (Shadowrun 20th anniversary, Rolemaster 4e, The Dark Eye).
(Discounting for the moment the cursed problem that you may be able to get people to play heavily houseruled D&D just because it has the name "Dungeons and Dragons" on it who wouldn't play a less houseruled version of something else).
Probably only if the base was whatever the current D&D edition is, though.
If you want 3e style high level magic, I'm not sure GURPS would be my choice either.
I'm not sure Fantasy HERO would be easier. But maybe.
To be fair, almost any other system is going to be a pain in the behind if you literally want the D&D magic system, because the D&D magic system is about the most ridiculously idiosyncratic and special-case focused magic system I've seen in any fantasy game out there, including even some other D&D derivatives.
That would be the goal for a D&D alternative, yes. Good chance I'd want to specifically run a Faerûnian sandbox.
I stand by the opinion its one of the things that feeds decision paralysis and people who really don't understand what their characters can do the moment the character hits even moderate levels.
There are certainly players like that.
I don't doubt if I was insane I could reconstruct both the general workings of D&D magic and even the individual spells in the Hero System using some ideas from the last version of Fantasy Hero.
The amount of work would be, to say the least, extensive and I can't imagine wanting to enough to do that work.
Yeah, that's why I gave up on the idea with GURPS in 2020 or 2021. It looked like more work than I had the patience to build.
But there are substantially more GURPS D&D conversions now than there were 5 years ago. I'd maybe be more willing to try it now.
I don't mean offense, but I think wanting a classless system and the D&D magic system in all its--glory--is asking largely for two pieces of rope that don't meet in the middle.
None taken, but I do think that Eclipse is a worked example of that, and that PF1e comes close to also being a clunkier worked example of that with its hyper-customisable classes + unrestricted baseclass multiclassing.
I suspect trying to make D&D work properly without classes would require virtually reconstructing it from the ground up, and I have no faith anyone could do it without balance problems galore.
it is certainly not a small task.