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.
Well, first, there is no reason to assume that even peasants in isolated communities speak the same language. However, I used to think like you do and tried to create a more realistic world. The problem is that a more realistic world sucks. RP with NPCs is one of the most fun aspects of the game. If you cut that off so that the PCs can't meaningfully interact with an NPC, it's not a win, no matter how much more realistic it might be. So as a practical matter, what you want is for every NPC that can RP or is likely to have non-violent interaction with the PCs, for it to actually be able to speak with the PC. This won't mean that they all speak common, but does mean that its in your interest as a DM to ensure the number of languages is small and that some sort of common tongue is shared with someone in the party.
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).
First, my definition of mid-level seems pretty different than yours. Raise dead isn't available until 9th level, even putting aside house rules that might limit how many clerics know each priestly spell, 9th level is IMO a fairly high level character. If such characters are reasonably common, the problem is that you tend to deprotagonize the PC's. If you've got lots of NPCs around that could easily handle any challenge that the PC's face before 5th level, it is in my opinion harder to explain how the world needs the PC's than it would be to explain how the world functions when some people can reliably bring others back from the dead. For example, in my current campaign (now in its fourth year), in the nation that the PC's started out in, there were to my knowledge only 3 characters of 9th level or higher - and none was a cleric. Three 7th level clerics represented the highest level clerics in the whole nation. So raise dead isn't necessarily widely available.
And to the extent that it is, it's impact on the campaign world can be reasonably construed. The general path I take is the 'Grimm's Fairy Tale' rule. In the fairy tales, evil villains seeking to assassinate socially important figures just about never attempt to simply kill them. Instead, they enchant them, or polymorph them, or curse them or do things that seemingly are less effectual than slitting a throat would be. But that perspective seems entirely reasonable if raising someone from the dead is a doable thing. So yes, assassinating someone important becomes harder and requires proportionally more planning and resources. But beyond that, raising socially important figures from the dead has a huge social and legal impact. For example, present real world law has a lot of provisions for inheritance, but no real provision for disinheritance. Once someone is recognized as dead, their wealth and titles pass to their heirs. Imagine the chaos resulting from the reverse, a legitimate heir losing wealth and title because their progenitor returned to life. All is well and good if this is a welcome occasion, but it's easy to imagine situations were it is not or where it disturbs the peace. For this reason, in my game most societies make it illegal to bring someone back to life if that person has legitimate heirs. In particular, returning someone back to life in a manner that effects succession is usually impossible by social custom. It's in fact easier for a peasant to justify being brought back from the dead than a king. The only exception tends to be if it can be proved that a relative coordinate the event in order to manipulate succession to their benefit. Society has a strong incentive to prevent any possibility of a succession crisis.
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.
Yes, and no. Very few low level spells exist with profound social effects. Probably the single most important examples I can think of is create water, create food, and cure disease. These spells have profound economic consequences, but we can mostly summarize them as - these societies are much wealthier than equivalent real world societies. And I would argue that (perhaps by accident and failure of imagination) that is exactly what we see when typical D&D societies are described. Poverty is something largely missing from most D&D settings. However, I certainly agree this is a big problem in some settings where magic is very common - for example, The Forgotten Realms makes absolutely no sense IMO.
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.
Well, that's certainly a trope of Forgotten Realms, which has probably the worst pantheon in all of fantasy. But I would argue that's not a trope of D&D generally, which often uses either real world pantheons or some better thought out polytheism such as the Lords of Heaven from Green Ronin's Book of the Righteous. Heck, your average home brew pantheon is light years beyond the FR in terms of philosophical depth.
I guess my point is that while I understand your frustration with all these things, I don't think that they are inherently problems or need to be inherently problems. If you are actually thinking about the clichés, you can easily subvert them.
