We all love D&D (we wouldn't be posting here if we didn't), but let's face it- there are some things about the game that we really don't like.
For me:
1. Everyone speaks the same language: I understand this for game reasons. However, it seems very silly to me that EVERYONE in the whole world speak common by default. I can understand a trade language, but the idea of a universal speech that even peasants in isolated communities speak is just absurd.
2. The prevalence of "raise dead spells": Any mid-to-high level cleric can raise the dead. Again, this makes sense from a game perspective, but this really puts a cramp in the internal consistency of most campaign worlds. Why should anyone fear death if they can just be raised later? Although the family of Joe Peasant couldn't afford to have him raised, kings and people in power have little to fear of death creating a powerful dynasty. Assassinations become much harder (since the person can just be raised as long as the body is intact).
3. High prevalence of magic, but no application of it: Although most D&D worlds feature absurd amounts of magic, most people still live in a psuedo-medieval society. If magic was as prevalent as it is in most D&D campaigns, I can imagine wizards getting together and applying it to society. Many people hate the idea of "magic as technology" paradigm, but if even the smallest hamlet has at least a couple of spell casters, why is all D&D magic seem to be centered around adventuring.
4. The default polytheistic assumption: I have nothing against the standard D&D polytheistic pantheon, but it seems to be getting a little cliched. What about different religious systems, such as pantheism (everything is part of the universal spirit), animism (worship of nature spirits), and even monotheism? One of the main problems of most D&D pantheons is that they seem so contrived. All the gods of the pantheons deal with adventuring and kicking-butt. We have war gods, death gods, fire gods, and nature gods for druids, but we usually don't have gods of fertility, or gods of the home which existed in many classical myths.
Any others?