Huh. Well. I agree that the third act feels the least 'finished', but at the same time I rather like the freedom of running around the city and finding new things everytime. I'm almost at 700 hours into this game and I keep finding new things or different outcomes.
And, I am rather content with the sidequests, really. I have to think real hard on one. I quite like how they are handled, and how some small bread crumbs lead to big game changers
[Nightsong, Ironhand Gnomes]
or highly rewarding endings
[Book of Thay, Minsc, Zentharim]
. There are also encounters and setpieces that I *really* like. Boaal springs to mind, the Swamp Tea house is brilliant, figuring out how to grab the that holy artefact in the monastary - super fun and highly rewarding. The final assault with the allies is lots of fun, and the underwater segment with the bubble-spawns is probably my favorite bit in the whole game; it is fun mechanically and the atmosphere is great.
So I have to think hard on something I didn't quite care for, or thought that needs work. But:
On these forums I make it no secret that I dislike the writing for the Emperor. With that, going to look for old house feels stupid, especially since he just tells you to go there when you walk past it. The quest design itself, though is fine; with the cellar and the encounters within.
Also, mostly for the same reason - Wyll's Act 3 Quest. Also because of how the quest is resolved; "Oh well, then it wasn't necessary at all."
Then. The Tribunal bit with the Throne of Bhaal callbacks. Nope. I didn't like that, and they did a serious disservice to beloved characters here, one in particular.