I also just finished the game. And feel quite sad. My ending was obviously the empress one...
I find this ending is the most logical and right. The girl has grown up, got the feeling of responsibility due to her numerous quests and adventures, left her punks friends behind and returned to her rich and loving fatther to work in his business. That's how it often happens in real life and it is the most real ending to my opinion. Of course she could stay with her punks gang and do graffiti on walls, but that would mean that she drew no conclusions from her adventures, and simply was stupid and irresponsible, which was not the case as we could understand that from the in game events. The girl grew up and doesn't need to run away from her destiny and is finally ready to face it fully, by becoming the empress and that's her fate. An empress with such superpowers than she posses is certainly a person specially chosen by the fate. And for her, I think the story just begins. She now understands and accepts her fate. While Geralt's story has obliviously ended in the grand scheme of things.
If you take into consideration that Ciri's decision to return to her father was partially Geralts decision, then it would perfectly fit his nature. What is the nature of a witcher? Kill monsters, be them humans or some magical creatures, and save humans. By letting Ciri to become empress he does exactly that. Ciri is idealist, and thus with conjuction of magical powers and political powers she becomes the most powerful weapon against monsters one could imagine. Thus, Geralt grants the world this weapon and he again fulfills his fate of a monster slayer. Indirectly. Ciri' fate is the same but on a larger scale.
This is my explanation of the Ciri ending and how I see this. Although I do not understand why did it have to be made in a SUCH a sad manner. Ciri doesn't die, nor loses her superpowers, but moves into a palace and continue her fate on a new, luxurious level. It could've been less sad, I think... But probably it was so due to her understanding that a big part of her life, the childhood with snow balls and funny things like bomb fishing, horse stealing that she wanted so badly... never happened, and now, it is certainly, will never happen. And that is sad, the sheer understanding of it. But there is a whole life ahead of her like I said earlier.
Actually, I think it may be that, Ciri story is a story of growing up, and saying goodbuy to your teen-age period of life, of becoming a mature responsible person, leaving your childhood unsatisfied wishes behind. Not every person completes that trial in real life...
I did not understand what happened in the last battle. Why did Ciri had to go to the tower with the elf and wtf they were doing there...
I also completely agree that the game should have been over at the Kaer Morhen Battle, Probably the last fight and the fight at Kaer Morhen were initially supposed to be two different options you can choose between. Like, fight in Kaer Morhen or take the fight to Scellige. And in the final stage of developpment they merged the two options into one to save on time. I would really not mind waiting another 6+ months and have the final game that is all from the beginning to the end on the level of the Baron quest.