The biggest thing for me, personally, that sticks out as a flaw, is that the Templars don't ever seem to get painted in a positive light, or at least, bare minimum, a non-negative light. I tend to be pretty neutral on the whole Mage/Templar conflict, and tend to agree with Vivienne as far as Circles go, but the odds just seem weighted in favor of mages in DA2. I side with mages almost every time, and the few times I did side with Templars, it left a bad taste in my mouth, because most of the evidence you see on the surface of the game is so pro-mage. Bioware seems to be a bit over-eager to offer a totally not at all biased approached to the oppressed mage flowers being harmed by cruel Templars as far as characters and quests go, which, admittedly, isn't completely untrue. We see blood mages, and then are told that they are the exceptions, that they are only doing this because they have no choice, whereas with Templars we see the cruelty, and then are told, that some, are in fact, good people, who do not abuse and rape and use the Rite of Tranquility as if it was no more than a party trick. Inquisition offers a more even view, but as far as DA2 goes, I think that most of first time players would side with the mages. Siding with mages isn't a bad thing, but siding with the Templars seems to be perceived as that in DA2.
tl;dr Unless you do every quest, read all the lore you can get your hands on, and play an anti-magic character, DA2 should be rebalanced so Templars get a chance to not look like the bad guys almost constantly.