The problems that I have with 3e are minimal. They are implementation problems rather than design problems but here they are:
1. The skill system. What are the odds of an average PC knowing something about his/her homeland. Hint, it's an untrained knowledge (local) check, unless they have the skill. Since it's a knowledge check, they can't do it untrained. How many PCs take the skill.
I wouldn't mind seeing some skills special-cased at the buying stage to maintain uniformity during use. e.g. I'd like to see languages expanded so that you get something like 5 points in a language for each point you spend on it, but this allows for greater versatility when applying the skill. You could try and decipher a scroll in a dialect or an ancient version, rather than knowing or not knowing the language. It bugs me that languages aren't treated like other skills.
It also bugs me that skills are capped at level + 3. What about crafters? Does that master blacksmith really have to be level 15 to do the amazing work he does? The cap is an arbitrary rule to prevent abuse that ignores the way the skills are used by the majority of the populace.
This is mostly to do with the way individual skills are implemented, and not with the system itself. That really helps, because I can just assign background skills (or level-0 skills) that PCs would never take, and house rule alternative skills.
2. Prestige Classes. I know prestige classes were never envisioned as the monster they have become, but I hate how the requirements force characters to metagame their progression plan to make sure they don't have to spend 5 levels making up the stuff they're missing to get into the PrC they want. I prefer the BAB +X or Cast spells of level X as prerequisites, because they arbitrarily set the power level you can expect from the class without forcing players to spend every last skill point and feat in a particular way to make sure they qualify at the right time (and if you don't qualify by level 10, you're pretty much screwed). I like to make role-playing restrictions for PrCs, and I can see certain skill and feat prerequisites, I just don't think they should comprise the bulk of the PC's selections.
I've got more, but it's time to go home.