Strictly IMHO, YMMV, etc. etc. -
Good Points:
-Accessibility: Folks who have never played an RPG can be up & running with a character and playing an adventure all in an evening. There are not many systems for which that is true.
-Publishing Quality: The WotC 3e books are more professionally done that a lot of previous RPG materials. Cleaner layout, better artwork, etc.
-OGL: the open license of the d20 system has given gamers a HUGE assortment of material to choose from. To quote Bruce Lee, "Absorb what is useful, discard the rest."
-Balance: The writers did a great job of balancing the player classes and races, for the most part. One or two could have been better, but nothing crippling or overpowering.
Bad Points:
-Editing: Despite the overall quality of the material on the core books, they could have stood some better editing regarding organization of materials. Too often a rule is explained, but in a totally different section of the book. That, or phrasing is left ambiguous on exactly what the writers intended with a rule.
-Legacies: A few mechanics that carried over from earlier editions and DnD's wargaming origins which, frankly, could have been improved upon; armor making you harder to hit v. absorbing damage, the nebulous nature of hit points, squares v. hexes, over-emphasis on combat, etc. All these things still work since it's the same for everyone in the game, but are bit abstact and make it harder to immerse yourself in the action.
3e is a good system and I prefer it over many other systems, but it does have its quirks and flaws like anything else. Of course, that which I criticize, someone else may applaud.