Here's my wishlist, I know the first two points kind of go against what you guys have already stated:
Make it fully 2d and be proud of it. Look at Rayman Origins and King of Fighters XIII for example, just beautiful.
Co-op multiplayer with turn-based combat like Fallout. (action points, ho!) Pausing to make decisions takes you out of the action and you generally have to pause a lot anyway, plus it doesn't work in multiplayer.
Just get rid of the laundry list-style questlog and replace it with a journal that holds essential information. It'll send a message that players have the freedom and responsibility of choice. If you don't remember the customs on how to address the king, obviously bad things will happen. If the king sends you on a mission to raze a village, maybe it's not such a great idea to comply.
The entire journey should be one of significance. It doesn't always have to be the end of the world, there can be personal stories or small incidents that only fit into the grand scheme of things much later. However, playing an errand boy in a fantasy world is just about as much fun as being an errand boy in the real world.
Players characters aren't blank slates. Make taverns that don't serve elves, have nobles scoff at your shabby clothing and farmers run or attack on sight due to that massive bounty on your head.
Draw inspiration from the act of (pen&paper) roleplaying rather than the number crunching system that enables it. I think what can be done with computers nowadays far outshines dicerolling. It's
that is so hard to emulate into the digital realm.
I hope I didn't sound too condescending, just throwing in my 2 cents. (figuratively and maybe literally once Paypal becomes on option) Neverwinter Nights 2 was a truly unique experience, great job on that!