-Novigrad's conclusion. This for me was the only area in the game that wasn't great all the way through. Velen, Skellige and Kaer Morhen were all handled perfectly well from beginning to end, Novigrad meanwhile was handled oddly. In the last Act, characters like Priscilla, The King of Beggars, and Cleaver all disappear off the face of the planet, meanwhile characters like Hemmelfart don't even make an appearance.
There are so many characters in Novigrad that it is not surprising that many of them could not be fully developed (well, in fact, all of them have problems in the final act). Even in the current state, Novigrad has more content than any of the other major areas (Velen, Skellige, Kaer Morhen).
Then there comes my biggest issues, the lack of a siege and Dijkstra going full retard. There was a decent amount of build up to Novigrad possibly having to defend itself from Radovid and/or Emhyr, yet you return to the city with Radovid hanging out there with ZERO explanation. Nothing! It felt like a missed opportunity to give the war storyline some extra tension and weight, and they could've given Dijkstra a better way of betraying Roche amongst a battle that's not out of character.
There is another thread that discusses this particular issue and how it could be improved here.