All I can think of for the reason behind DA2's unfocused story is that it was there to set up the scenario for ME3, which will now have a clearer goal: to resolve the mage-templar conflict, and save ferelden and the free marches from being torn apart by an all-out war.
If DA2's setup isn't used in the story of DA3, then I'll be very confused - then DA2's story seems to have been left on a kind of a cliff hanger, without resolution, and it would seem pointless and rather frustrating.
I think that the kind of story DA2 had was something of an experiment by Bioware on how a story that didn't have a clear over-arching fantasy "save the world/kingdom/princess" goal from the start would work, and how it would be received.
I don't mind experimenting with story structure, but I'd chalk this experiment on the "didn't quite work" column.
That said, I don't view DA2 as quite the failure many people see it as - it has severe flaws that have been pointed out by many people including myself, and is a pale shadow of what DA:O was, but as a stand-alone game, if we don't compare it to it's predecessor, it's decent enough, and does have some positives as well. (Like character writing)
I fully agree with the OP though that the game feels like a series of sidequests - when you look at the journal that differentiates between side quests, companion quests, and main line quests, at any given point, it's baffling to the first time player why some quest is a mainline quest while another is not.