The absence of skills. I know many people found this irrelevant, but I was terribly confused about it. I completely disagree with the reasons adduced to justify it. Since I really like to work on characters with strong diplomatic skills, the poor implementation of it on "Hawke's character" and that thing about letting companions speak for you made me feel very unconfortable. Even on Mass Effect 2 we had to spend some effort on build up diplomatic dialogs.
The fixed dialogs with companions. Some people say that dialogs are better presented with DA2 system, but I completely disagree. The sole opportunity of initiate dialog at will makes companions way more deep and plausible. I'm not saying that dialog was perfect in Origins, but the idea they came up with DA2 is worse in almost every aspect.
Wave system. I can't understand how anyone could have any fun with this. I really like the fast paced battles, but constant flow of enemies coming from everywhere made me uncapable of having anything more than two playthorughs. And the second one was very frustrating. The worst thing about this is that some battles are actually very fun in the first wave. But after that, one wonders... why they have done this?
Re-used environments. Little to say about this. Discussed way too many times. It made me feel as if I was playing a self programmed game on my MSX. And I am a horrible programmer.
Equipment. Tons and tons of useless things without any kind of description and sometimes, even with the same name and different properties. I like when I find standard equipment or useless weaponry, but the absurd amount of almost-random pieces of crap on DA2 makes me feel dizzy. How is that Im not able to understand why is this an imporvement over Origins inventory and equipment system? And let's forget about the important items that are not present, have a weird question mark icon, or are treated just as "trash". So, the elven keeper gives me an important book with lot of meaning... and is crap? What the...?!
Teleporting mages. Im sorry, but I don't buy the explanations we had about this. Seeing mages teleporting was one of those confusing and disappointing moments on DA2 for me.
Simplified secondary quests. Secondary quests on Origins were pretty poor. But in DA2 are even worse! I don't get it. The worst of the bunch are those about giving random objects to people, but also the "big" ones, as those that involve killing some important demons. DA2 could have been brilliant just by refining this, because many of the quests had lot of potential on them.
Restricted weapons and styles. When I started my second playthroug as a warrior I was very excited about creating another dual wielding sword fighter. Imagine my face when I discovered that warriors are "unable" to fight with two weapons. But not only that... they cant equip bows or crossbows! And even more... all weapons are restricted to their native class! Again, I'm unable to understand the positive things about this change. Following OP expression, it made scratch my head and say "Huh?!".
New artistic design. I'm sorry, I don't like the new art direction. As I have stated many times, I think changes in graphical and artistic appearence should be way more subtle. Animations, armors, weapons, persons... everything seems absolutely out of scale. As I said, I like the fast paced comba, but the animations that give form to it are ridiculous, for example. Elves look like pale beggars with donkey ears and horrid noses. Flemeth... well. You get my idea. I simply don't like those changes.
Well, probably Im forgetting something, but thats all for now