I'm surprised at the discussion that's arisen from this.
Yen trusting Emhyr - there's no reason not to trust him, he had his chance in the books to fulfill his plan, he refused to do it of his own volition - i.e. if he wanted to harm Ciri or Yen or Geralt, he would have done so long ago, when he had the upper hand. Yen is ambitious and wants what's best for Ciri - being the empress of literally the known world is not a bad position - so she encourages Ciri to cooperate with Emhyr.
That said, Yen has always been very controlling and Ciri has always been free-spirited. And she likes to overreact. That's the whole "Yen plan" line right there. Ciri doesn't like being forced into things, Yen pushing her to listen to Emhyr is interpreted as scheming as a result - it's not the first time in the books or game that Ciri behaves in this manner.
As to why Ciri does what she does in the Empress ending - she's very much an idealist and taking up that burden is the grown-up thing to do. It's the 'responsible parenting 101' ending. If Nilfgaard wins and the player has given Emhyr a chance to extend his offer to Ciri by taking her there before confronting Imlerith, she takes up Emhyr's offer. Because she's no longer the teen that longs for freedom and adventure - that's the result of the player's parenting as Geralt and encouraging Ciri to see Emhyr.
If you as the player push Geralt into supporting's Ciri's more free-spirited nature and don't take her to Emhyr, she follows the more dangerous and hard life of a witcher, but that's her passion.
Like I've said before, TW3 is one big parenting course, more or less, and the whole game is focused on this.
Also, "plot holes" is a term that's being misused a lot in this thread. Plot hole is not a term to be used to mark plot events that you personally disagree with, that you think are cut off too soon etc. A plot hole is an event that occurs that contradicts what's been established in the story and the 'rules' that govern a fictional world.
Same goes for "bad writing". Writing that does not align with someone's expectations of the direction a story would take is not the same as bad writing.
On a moderating note, @
Charcharo If you could stop insulting gamers' intelligence, that'd be swell. Think whatever you wish to think about the quality of the story in the books vs. that of the games, but please stop disparaging the "gamer" crowd - that's against the forum rules and will result in moderator action if it continues in your future posts.
And to everyone else, drop the ad hominems, please. Specifically referring to personal attacks aimed against certain users that have occurred in this thread. Try to be more civil in your discussions.