1) At its core, it's a game about invading peoples' homes, killing them, and taking their stuff. While it's of course possible to construct scenarios where it is morally okay for this to happen, it's also really really easy to ignore that and accidentally paint the protagonists as the real villains.
2) To justify point one, the game goes out of its way to handwave the victim status of the former group by presenting them either as Animals, Abominations, Unthinking Automatons, or Baby-Eating Sadists. But D&D loves its large bestiary, so the game shoehorning in all of these sapient critters into one of these four categories gets depressing after awhile.
I think that it's time for the game to really rethink its core paradigms. I mean, shit, when the fucken Super Mario Bros. is ahead of you on the morality curve, it's time to redo your franchise. So here's my list of suggestions for D&D.
- Get rid of battle-based experience. 3E and 4E's way of trying to avert this was bullshit because even if it didn't directly endorse murder it endorsed brinksmanship that very likely lead to combat. Characters should only get experience for completing an objective or adventure. If they get clogged down in unnecessary fights on the way to complete it, then tough cookiepuss.
- The game should default to non-lethal damage. Yes, I know it creates the 'I knocked the orc out with my +2 Reaving Longbow' silliness, but if you give players the default assumption that their enemies live if defeated and that you actually need to go out of your way to kill them, players will be a lot more thoughtful about it.
- Most sapient critters should be able to be reasoned with. Unless you have an irredeemably evil race like balors, you should be able to talk/bluff/intimidate your way out of most fights.
- If you're going to have evil sapient critters capable of moral choices, the game should make it clear that they're evil because of their upbringing and not race. Not only will this stop people from slaughtering the orc raiding party who just wanted to get some food, but it also makes killing the actual evil bastards more satisfying. No one really gives a shit about taking out Random Mook #32, but people will line up around the block to stick a sword in Luca Blight or Szass Tam.
- D&D needs to make it so that most critters will run or surrender on losing odds--this includes if they think that they're outmatched. It makes players feel badass if they see the ogre army crumble and head for the hills if they recognize the PCs. It makes the PCs feel badass if a lizardman chief approaches them respectfully in the woods and offers them peace in return for respecting the forest.
- D&D needs to make it so that critters are actually easily convinced to abandon their evil ways. Even if you take out the band of deserters nonlethally and tie them all up, what are you going to do with them? You could leave them to die in the woods, which is just as bad, or you could go through the inconvenience of carrying them around. Or you could just tell them that if they swear allegiance to your Lord and give up their evil ways, they have a hot meal and a pardon waiting for them in your hometown and here's a symbol showing that they have PC protection.
- D&D really needs to stop that whole 'less pretty races are less advanced and more violent' bullshit. In the next campaign setting, the Mountainhome Alliance should be composed of goblins, halflings, humans, dwarves, and warforged. The Forest Federation should have elves, lizardmen, orcs, birdfolk, and aasimar in it. Seriously. And unless you're specifically trying to paint a society as evil, they should have critter intermixing.
- Evil societies need to be as evil as you can get while still maintaining a PG-13 rating. This means going a bit further than Nazi Germany. The best way to do this is to implement a Halo-style caste system with the upper echelons being multicultural or being headed by actual demons or gods or whatnot.
- People actually need to see rewards for being good. Your party should be PROUD of the fact that they've defeated over a thousand foes without killing a single one. They should take PRIDE in the fact that they're the only ones the Sahugin will listen to because they've treated everyone fairly. As it is, D&D is a wasteland of nihilism and greed and that just generates a 'fuck it, even if I kill all of these dragons no one will give a shit' attitude.
- Because people still like killing shit, the Monster Manual should have a lot more critters where it's actually acceptable to kill them on sight without thinking about it too hard. When you destroy a sentient golem, you're actually doing it a favor because you're releasing the tortured elemental spirit. Killing a Dire Wolf shouldn't make PCs feel bad about harming nature because they're stupider than chickens and attack everything else on sight for the lulz. Ghouls literally have no purpose in life other than to harm others; kill them and feel good about it. A lot of critters, like demons and mind flayers, are actually composed of concepts like greed and sadism--destroying them doesn't even kill them because they'll be back in a few years and they have a racial hivemind anyway.