So far the major story related complaints I've seen are:
-Karlach's Ending and questline -Upper City (I don't see this coming back tbh, Act 3 is long enough as it is) -Lack of Minthara content -Asterion's Ending -Lack of epilogues -Bad ending choice in regards to the Emperor and Orpheus -Adding some more romance scenes
True, also I don't know how the situation is with Halsin, Minsc and Jaheira, I'm expecting that their fans also want as much story updates as possible. This could possibly also take some time