I agree with Voadam, in that I think it is really a complicated system, and high level combat can really get bogged down in number crunching, especially when lots of high level magic is involved. Really nasty stuff. I had to start brining a calculator to my last game sessions, because those creatures put out so much damage that it just got to be too big of a headache otherwise.
But there's a bit of a dichotomy going on here. I see some people talking about customizable rules, etc, but are the really really all that customizable, as opposed to say GURPS? D20 just doesn't work everywhere, I don't think. I mean, in the game I'm currently playing in, I'm playing a cleric, and I asked the DM if there was ever going to be undead in the game. We hadn't fought any or seen any, and we're 3rd level. So, I have this ability to turn undead that I haven't been able to use, and if I was never going to be able to use it, I wanted to have the option of replacing it with something else. But D&D doesn't really let you do it very easily. So, D&D isn't very portable - the characters are designed with a specific world type and makes certain (*gross*) assumptions about the kind of game you'll be playing in. All the CRs are adjusted to this, all the monetary values are adjusted to this, all the class skills, and modifiers are all adjusted to this. To modify them, or to place them in a world where these assumptions don't hold true automatically makes some classes more powerful, and other classes weaker. Players don't get the option to choose their abilities based on your surrounding. So, you could eliminate undead from your world (not so unrealistic) and then you've just shafted your cleric to some degree. The rules don't easily support that.
I guess what I'm driving at is that some of the classes have *fluff* inherently engrained into them as part of who they are. Clerics turn undead, and druids summon animals for example. So, for me, there is fluff in the system, but it's not the right kind of fluff. A good system should be portable, and world-independent. I should be able to make a balanced cleric in a world devoid of undead, for example. The fluff should add flavor to the rules, not constrain the rules to the world.