However, it has one glaring flaw for me. It's too much work. From his own admission, he's got hundreds of pages of house rules. In order to do this, you'd need to rewrite every single class, spell, and monster in the game.
No, there is no need to rewrite everything or anything. In fact, if that's your whole issue, then you need rewrite nothing. Most of my rewriting has nothing to do with playing at low levels, where, mostly things just work in 3.5 anyway. Much of the rewriting is to ensure that if I do go into the double digits, things will still work. Beyond that, I probably have about 20 or 30 different issues I'm trying to solve.
1) 3.5 has too many rules spread out among too many splat books. I'm condensing everything I think important in 3.5 including char gen into a smaller subset of rules.
2) 3.5 has poor balance, and is easily broken to produce scores of pun-pun like things. This requires a tacit table agreement not to break the system and even an understanding about what power level is acceptable. I far prefer to say, "If it is in the book, you can play it."
3) 3.X in general had too much slavish adherence to conventions of 1e because they needed to reassure the 1e crowd that this was still really D&D. An example of this might be the fact that Barbarian, Ranger, Paladin, Druid and Monk were core all classes in 3.X. Another example is seen in the Leadership feat, maintaining 1e's primitive exception based notions of the relationship of the character with the world.
4) Where 3.X departed from 1e it was seldom out of understanding why 1e did it that way or what the consequences of the departure would be.
5) 3.X never addressed issues like the broken economics of D&D, continuing to price items according to dungeon utility and balancing spells according to their utility against monsters or in solving dungeon problems without attention to their impact on society and economics.
6) 3.X had a lot of process ambiguities like what it meant to 'search' something.
7) 3.X was far too tentative about providing power through feats and skills while being extremely generous about providing power through spells. This and several other changes made spellcasters just far more attractive in the long run than non-spellcasters.
8) 3.X's base classes were a hodge podge conceptually, with some classes being extremely generic - fighter, rogue, or to some extent cleric - and other classes bringing with theme tons of real world baggage, setting trappings, baggage from prior editions, and other unnecessary assumptions. This resulted in all sorts of crazy patching through alternate classes, prestige classes, and additional equally narrow 'base' classes.
9) 3.X's math begins to break down near 20th level. In particular, save DC's bloat way too fast especially for high CR monsters. There is too much save and die with low percentage chances of avoidance at high level, leading to battling immunities.
10) Speaking of immunities, unquantifiable (and therefore infinite) power was itself was something that needed to go.
11) Several of 3.X's skills were odd or left largely undefined. Profession is a good example here. A good overview of the problem can be obtained by examining third party supplements and the different incompatible approaches that were used to try to deal with ambiguities in the skill system.
12) The fighter class in particular didn't do what it said 'on the box' and generally made everyone unhappy. There was also relatively poor provision for playing skillful characters that weren't 'the thief'.
13) My homebrew contained ideas that weren't supported by default - fey PC's, Orine, Idreth, mariners, etc. There were things that I was doing in 1e that no longer worked in 3e and didn't have good counter parts.
14) The 'housecat' problem (should farmers fear their cats?), and by extension the larger 1st level problem (1st level isn't part of the traditional 'sweet spot').
15) The tendency of PC's to die through no mistake of their own, just simple dumb luck.
And so on and so forth. If you want to play my game, I can give you about a 500 page document. If you want to play 3.5 just as a player, how much text does that encompass? All the core? All the 'complete' books? Where do you stop?
I can't recall any RPG system I haven't wanted to 'beat into shape' though. Chill 2e maybe, though I didn't run it, just play it and frankly never really understood the rules completely. Luck seemed to much of a god stat though, and I was never really happy with the brawling/martial arts separation.