...so, after 55 hours of searching for Ciri, finding her, caring about her, and finally defeating the Wild Hunt, I'm sad and disappointed.
This game sometimes is not that clear when it comes to consequences of your choices.
You made a mistake when you just wasnt in the mood to play snowball... you´re playing an RPG, so you should have put yourself in the character, and not let your real world lack of patience to roll over what was happening in the game.
And you acted like her father, when you should have acted like a witcher, because Geralt would never live as a couple with Cirila just to protect her. That totally wouldnt have anything to do with being a witcher. They have a very hard training because their lives are hard, and no witcher is expecting that other witcher might be forever in need of something.
They must be independent and have a strong mind to take their own decisions and pay the consequences. By acting as a protective father, you just let that slip, and for the game´s understanding, you didn't inspire Cirila to become confident enough to take her decisions, so she´s feeling sad in the end.
That is totally true in terms of life itself, but of course the videogame lasts only hours, so there´s no time for too much debate.
About the emperor, the game puts us against him.... unless you´re the "i dont give a shit to nothing" kind of people, but in the end you realize he just couldnt stop her if he wanted, and he´s her father and for a long time he had his daughter completely missed in a world where you have horses transporting letters, strong magic, and people just vanish from out of nowhere. It´s not like today when you can move an entire tv network to help on your kids disappearance. So as Geralt had some paternal feelings for her, he said (but he´s your father... when she rejected at 1st).
As I already had finished Witcher 1 and 2, I looked for some orientation to not have this bitter taste you had when you finished it.
You can reload a past save game and replay to make the ending that you wish. I know it´s gonna take some time, so good luck with that.