1. We definitely need two scenes around the ending where we can talk to our companions, like a "calm before the storm" scene and then a post-battle closure thing. Acts 1 and 2 both have post-battle closure scenes.
2. The choice to trust the emperor or not needs to have structural consequences. There should be a different finale/climax depending on what we chose and the ending choice should also be different based on what we chose going into the ending.
3. There needs to be some kind of big stakes-raising reveal with thematic implications. The "someone has to be a mindflayer" reveal doesn't cut it. The obvious candidate for this is the motivations of the dead three and the question of mindflayer souls, which Withers mentions at the end of act 2 and then is immediately dropped as a plot point.
Several people have mentioned Dragon Age Origins but I also want to bring up Cyberpunk 2077 which has in my opinion the best branching ending of all time. In that game the climax is substantially different depending on your choices and there's a big heavy thematically resonant ending choice and several long epilogues to show the consequences of that.