The idea of Dragon Age II was to show the worst of both sides. Meredith and Alrik show the worst of how the Templar Order's power can be abused, and Quentin and Tarohne show what the mages can do if they aren't watched by someone. Then we have Anders and Orsino, who show exactly what the Templar abuses lead people to do. Finally, Cullen and Alain round this portrayal out by showing that there are semi-reasonable people on both sides.
I got the best part of that message from my companions alone. I didn't need to be hit over the head constantly with it from the whole city. All of companion's personal stories and attitudes were done well (Fenris, Anders, Merrill), but I hated the insanity of Kirkwall itself. It got to be too much. I liked Kirkwall when dealing with the criminal underworld, playing the part of a lowly refugee, kicking Qunari ass, etc.. There should've been a little more of that to round it out. Like more crime or raider quests with Isabela, for example. There's too much damn magic in Kirkwall.
Perhaps the best side story however is Thrask and Grace, and how that eventually became a mess. The message behind it was sad, but wasn't too ridiculous... How all of those mages and templars finally worked together, only to have you and Grace sabotage it in the end. lol
edit: Sorry if I'm getting too off-topic. If Leandra had to die, I wish it hadn't been so senseless.