I would argue that the plot holes in the game would require pretty intensive, all hands on deck work to amend. To really excise the plot holes would require them to go through and changee every part of the story, tweak pacing and quests, remove stuff, add stuff, probably make a whole new opening sequence, it would be a lot of work that's honestly probably not worth it when it seems that the unanimous opinion of players is that there's nothing wrong with the story, and Larian does indeed seem to be happy with the story that they created. They really shouldn't be, but when they're sweeping awards left and right, I can't really blame them for thinking they've done a good job.
Yes, I think to improve the story so that it actually makes sense would require an extensive rewrite. Personally, unless they make the emperor cutscenes optional (as it was in the EA with the dream person), it's not a story that will interest me anyway. I'd therefore rather they focus on improving (or in case of Minthara fixing) companion questlines, because their content is at least more engaging.
Though I would not mind a dunegon crawl dlc, like the original BG games had.
