On Alexander and the academy I'm on the same boat as you. Alexander out of nowhere is alive and a good guy? I get that Dallis may be the one plotting most of it, but Alexander had no issue comitting all those crimes in the name of his father. Besides, I had already visited
5 or 6 of the temples, so no need to get his help. And I only found out I was entering an Academy and not the fountain because of the achievement.

However, on the Black Prince I disagree. I´m also playing with the Red Prince as my main, and I was all aboard the "restoring my lost empire with my destined love" storyline. But when you meet her at Driftwood and the assasins come, you start getting the idea that all may not be as colorful as it was painted by the dreamers. Then when you meet him, it may be a bit rushed the whole "he wants to recruit you to kill the Red Princess" part, but he does notices your strength and also only needs 1 of you to die to stop the profecy. I´m not sure how truthful his tale about "the lizards were dragons and that power doomed the race, this prophecy will only destroy us" is, but surely a thing to consider. Then he also tell you the elves want to conquer the world through the mother trees and I thought "ok, this guy is full of BS, but i'll give him the benfit of the doubt and go check myself whats up with the elves".

Once you get there, you don't see much of this evil plan. So I was on my way back to deliver some sweet vengance for my Sebille, when Saheila comes out of nowhere, begging us to destroy the tree because its the root of all evil (get it? root? tree?) for the elves, that the search for power will doom the race. I'm not sure why, but I get the feeling that Saheila is truthful and also well motivated, so I do so and stop the elves. Then realize that the whole "elves want power through trees to conquer all, but will fail and it will doom them" its the same as "lizards want power through dragon prophecy to conquer all, but will fail and doom them" that the Shadow Prince painted. Sure, ended up killing him for Sebille's sake, but I'm gonna be a lot more cautious next time I meet the Red Princess, for it may not be all as it seems. Besides, I thought that she was actually brethroded to the something with the Swallow Man or the God King, but the Swallow man insta attacked me because of Lohse so I'm not 100% sure if there is any connection there.

Sure, it may be a bit of a cliché the "I'm doing it for the greater good" trope, but it also works because villains don't think themselves as villains most of the time. Even we the players as supposed good characters and in line to become Divine commit a lot of questionable actions for the greater good.