Finding out Edelgard was the Flame Emperor was legit uncomfortable. When the big choice came, I didn't like neither Rhea nor Edelgard. But in the moment I sided with Edelgard because Rhea seemed to have something planned for Byleth and I trusted her even less. I also got the sense that while she associated with Arundel's group, she herself had different motives to them and didn't like them very much. I did believe her when she said earlier that there are different motives in play. That said, when I started fighting against the church, and fully realized what her ambition entailed, I was like:
I felt like I was Darth Vader killing younglings when I killed Flayn. Really though, having to face the former class mates as the enemy after the time skip is brilliant, and legit uncomfortable. It is great that they added moral ambiguity to your actions and have you join the instigating force. Even more so when you realize that Edelgard made a deal with the devils who tortured her.
I was going to romance Edelgard at first, but felt bitter enough towards her that I ended up romancing Linhardt, which had the hilarious side effect of Caspar ending up with Edelgard somehow. I don't understand how these work, so I definitely did not intend for that to happen.
Regardless, Edelgard ended up being my favorite character. She is so right and so wrong at the same time.
I wish they would have tied up the loose ends better, but I was happy about it nonetheless. I liked it better than the BE - C route I took afterwards. Although that Shambhala level was pretty cool. Honestly though, they would have been better off dealing with Those Who Slither in a sequel or something, and hence why I felt better about E route. I think that dealing with them in that one battle is just anticlimatic. Heck, that was my problem with the church route, it just felt anticlimatic. Its just that nothing about Rhea gives me reason to root for her even if her side is better by default in that she didn't start a war that killed many, while Edelgard is written well enough that part of me wanted to follow her ambitions.
The biggest thing that hamper the story imo is Byleth. Firstly, I want to say that at least the player avatar is used well in that they don't overtly influence the plot and instead guide the house leaders. Meaning all agency is on the house leaders, which is good. But Byleth needs more. They need actual dialogue, they need to be a little less special, and I wish there was the option to act bitter even to the people you sided with. Byleth needs to be more of their own character. If they were, they would focus more on the way Edelgard was the indirect cause of Jeralt's death.