I proposed once that the flashbacks with Thaos should've been playable, to make them more personal. I think they tried to copy BG1's story structure -> You find yourself not knowing what you are (Bhaalspawn/Watcher) or where to go, a central conflict (Iron Crisis/Hollowborn Crisis) sweeps you up and introduces you to your antagonist (Sarevok/Thaos), you go around trying to get to a big city (Baldur's Gate/Defiance Bay), a political struggle (Iron Throne/Animancy) and coup makes itself apparent (Sarevok trying to kill the dukes/Thaos killing the duc), you go around trying to catch the antagonist (Thieves' Maze/Sun in Shadow). All the while unrelated adventures happen. The execution differs greatly, however, and PoE struggles with coming up with a plot and making the characters in it relevant. It tries to focus too much on each premise, but since it's simultaneously rushed and overwritten none of them can be given a spotlight, so the narrative jumps from one to the other without any precedents.
There is no problem with each of these premises or whether there's an antagonist or not. It would've turned out better had the story been focused on one thing, the game is already bursting at the seams by trying to do too much with a limited budget and time constraint. They could've interconnected everything better, but that would require either more time/money or cutting of different content, like Twin Elms. Which I wouldn't have been opposed to tbh, Twin Elms feels like and is an afterthought. There is an extra act which BG1 doesn't have and could've been cut without the game losing anything, and even gaining something. If one game could benefit enormously from an EE, it's PoE, I kinda hope they do do this at one point.