This title won't invite flames at all.
Having said that, I think D&D 3.5 has several warts, notably:
- Attacks of Opportunity
- A number of special rules combined with Feats to ignore said rules
These are known problems, and D&D 4e will explicitly address at least the first two.
There's no reason you can't design a streamlined combat system around the d20 mechanic, on a par with GURPS, Basic Roleplaying, or any other system including PDQ. Star Wars Saga Edition and True20 have apparently done so, although I haven't played either to verify the claims.
"On two occasions I have been asked [by members of Parliament], 'Pray, Mr. Babbage, if you put into the machine wrong figures, will the right answers come out?' I am not able rightly to apprehend the kind of confusion of ideas that could provoke such a question."
- Charles Babbage (1791 - 1871)