BG2 is my favorite game of all-time. But DAO is my favorite game since. I haven't finished yet, but I've been doing --nothing-- but playing the last week. I mean, I'm barely eating or sleeping, it's crazy. I had to take a breather and what am I doing, I'm looking at the DAO forums for crying out loud. Comparing them...
Characters: Even
Morrigan, Alistair, and Leliana are as endearing as Minsc, Viconia and co. I hate the "<char> approves +5" popups though, it completely ruins the immersion and encourages reloading when a dialogue doesn't end as expected for the player. Would be nice if DAO companions would initiate important conversations on the road so I don't feel like a paperboy in camp.
Bodhi and Irenicus are better than the DAO main bosses. I guess the archdemon is a sort of Sauron-like figure, but it isn't persistent enough in the story to be effective. However, I really liked the sub-bosses in DAO, very creepy bunch. I never really took the BG2 sub-bosses too seriously besides maybe Firkraag.
Plot: Even
BG2 was more personal and had a better main plot (expansion excluded), but DAO has better subplots in that there are many ways to finish a quest. Just finished the Urn quest and really liked the double-cross.
Combat: BG2
DAO feels like a chore compared to BG2. You can only queue 1 action, the camera can't handle narrow spaces like alleys, lack of camera control options, companions that stand there taking hits because the AI can't figure out what Enemy Nearest - Attack means, warriors that courteously wait for the enemy to get up after knocking them down, lockpicking as a combat talent, useless spell descriptions. Sorry, don't mean to gripe, but I think the combat system is the most disappointing part about DAO.
Overall, I would say I'm enjoying DAO as much as BG2 from a storytelling and exploration perspective, but I can't say I ever look forward to the action elements in DAO. Improve that, and DAO would quite possibly be my new favorite.