SPOILER ALERT
Yeah, I got the ending where Yen and Tris both dump Geralt. However, I am happy that Ciri died and Nilfgaard won. I hated Ciri and really like Nilfgaard so 2/3 isn't bad.
But yeah, this is a problem that LOADS of people have an issue with. You'll find a huge campaign on the forums aimed at bringing back the characters after the story. This is because after you finish the storyline, no matter which ending you get all of the main characters are deleted from the game apart from Zoltan and Dandelion. It's probably because CDPROJEKTRED didn't have enough time to finish up before launch. But to answer your question, nobody is in the game apart from Zoltan and Dandelion once you finish. They get deleted.