I really liked the Inquisitor story...it's my favorite of the 5 I've played so far. In fact, it's the only one I've played twice, just because I enjoyed it that much and wanted to experience it again. That said, I do have two kind of notable beefs with it:
1. Too much time spent on healing at the beginning of act 3. I would've been fine with one or the other, but focusing o it for both Belsavis and Voss was a little disappointing. Dedicating one of those to gaining a following of disciples among the Sith (and incorporating Xalek into that, so that he joins a little earlier?) would've been great.
2. I would've liked a little more opportunity to get friendly, or at least acquainted, with Thanaton. He was a pretty cool guy, really. After the time or two he makes contact in chapter 1, I (and by extension, I suppose, my Assassin) thought he was a pretty cool guy. I think that the lightside/darkside ending, rather than being about freeing the ghosts, could've been cool as to whether or not to find a way to ally with Thanaton. I think that could've reflected the whole politics and subterfuge feel that the writers were supposedly going for, too.
Also I think Kaal and Corrin are wasted, they got involved much more than Xalek.