So I don't think the it's a problem that the plot is hard to put together - it kinda fun to put together and talk about in the forums. But imo it is a problem that the player is not rewarded for piecing it together. Once you have read Gortash's notes and put everything together you should be able to challenge the emperor.
Did you tadpole us? Did you purposefully let the tadpoles change our brains?
Even once we uncover the emperor's evil doings the game assumes we trust him. Indeed fans on Reddit call the moment you release Orpheus a 'betrayal' but that's a misreading. Pawns cannot betray their manipulator, they can only free themselves from his machinations.
That's a general problem with the character of the Emperor and the game's story at large. For all the game's freedom of choice, the main story doesn't do much to respect your decisions. You can find out all the game's secrets in books, letters etc. but it rarely gets reflected in the actual dialogue (Kagha being the exception that proves the rule). With the Emperor in particular, "reactivity" is practically non-existent and most of the choices you get to make in regards to him simply end up not mattering at all. That wouldn't be a problem if the role he plays wasn't so absolutely integral. In retrospect, it would have been prudent to cut the character from the game and have us be protected by the prism itself (some dialogue still hints at this being the original vision) and spend more time on the characterisation of Dead Three's champions. It would have made for a more focused experience. With the Mindflayer stuff being as unengaging as it is, the Emperor appears mostly as a distraction that gets more frustrating with every playthrough.
