I liked DA:Origins quite a lot, for the most part. That said, my biggest issue with that game was the huge disconnect between the game world and the game mechanics. Like, how you could throw blood magic left and right, and nobody would care, except everyone would be all "but that other guy is a blood mage, you must stop him!" Heck, you could turn the game's most adamant anti-blood mage character (Wynn) into a, you guessed it, blood mage. Because character system wise, blood mage was just another specialization. Or, to use another game (Skyrim in this case), I really hated how the game didn't know which factions you were part of. Unless it was important for a specific quest. If I can become the leader of virtually every faction in the known universe, some interaction between those factions would be quite nice.
The easy way to handle this, of course, is to not have a game where any of the mechanical character choices should have a significant impact on the game world (eg. if everyone hates necromancers and the main plot involves killing all necromancers on sight because necromancers are bad, don't let me play a necromancer who can walk around town with a small army of undead in tow).
The cool way to handle this, is to have a game that is actually aware of the in-game choices you make and have a world that reacts accordingly. Of course, that might be tough to pull off. But it would be pretty cool.