Well i have to say, that all those issues you've mentioned come on top of my frustrations with the quest plot.
You are right: The City itself is made very well. The characters are wonderfully designed. I love the Story in itself (finally!). But just spending hours on the same fight you have mentioned with those Skeletons and still they Keep coming no matter what you do is just frustrating. That alone would leave me with a stained Feeling of the whole game.
So it really Needs ... polishing ;).
I wanna say, that the game is just so really well done that it deserves to be as Close to perfect as it can be with those few, minor tweaks needed.
Cheers