Facial animations are a forgivable sin if the voice acting is good, the characters are likable, and character designs are well-done.
The problem is that all three of these fell short of the bar set in previous games. Even though she eventually grew on me, Sera's accent is still pretty quick to get on my nerves, Vivienne is a stone-cold ***** throughout the whole game for no good reason, and they would've been better off making Cassandra look more like her incarnation in DA II, instead of just making her look dour and severe all of the time. I know she's supposed to look that way, but they could've done it without making her so...ugly.
(Also, I don't care for bald women, at least give Vivienne some hair.)
There's simply not a character in this game that I really, really like. In the first game, it was Shale. In the second game, it was Merill. But there simply isn't a comparable character in Inquisition, and with Bioware's efforts falling short of past successes, I started noticing things like the facial animations a lot more than I would otherwise. It's never truly bothered me before now, and I think it's because I'm seeing more of poorly or lazily-designed characters that I don't like.
Making good, interesting, likable characters will make up for a lot of shortcomings.