SPOILERS
I went with Ciri as the witcher and Geralt still on the path but living in Kovir with Triss. I have to admit, Yen wore thin on me quickly with the attitude towards Geralt. It just never seemed a healthy relationship to me. Still, wish Shanni could have made it from the first game 
I still wish we got to play more as Ciri since her and the Wild Hunt were the most important aspect of the game. At times, I felt a bit detached playing as Geralt and not seeing much of the Wild Hunt.
I can get where you're coming from, but it felt a lot more compelling to me to be this father figure looking for his daughter who he clearly cares a lot about. I had so many feels watching Geralt every time he learned something new about her whereabouts and even more so when they were reunited and had those little moments together. Plus, I liked unraveling her story gradually as you went along.
As for Yennifer, she could be a little controlling and harsh, but I feel like a lot of that stems from her having to be that way to survive in the past. She's blunt and doesn't sugarcoat things or baby Geralt. She's secure and independent enough to want Geralt without needing him at her side all of the time. She's also not a damsel in distress who needs Geralt to save her. She doesn't *need* him, but she chooses him. Plus, Geralt has been doing her best friend for a while so she was clearly hurt. Maybe he didn't have his memory at the time, but if you were in her position, you would probably be at least a little bitter about it. And that same point is why I find it hard to like Triss. She KNEW Geralt and Yenn had been together for years and years and had this almost adoptive child together in Ciri and yet she still manipulated the situation to be with him. I have no doubt that her feelings for him were real, but it's still f*cked up to do that to your two best friends no matter how you put it. Plus, despite what happens (happened) Yen forgives Triss and remains friends with her. I don't know about you, but I definitely couldn't do that, so Yen clearly isn't the stone cold b*tch she wants outsiders to think she is.
I think if you read the books, or at least a few of the stories involving Yen, you'd see her in a much different light. I know I'm going overboard defending a fictional character, but I have a lot of feels and I think Yen gets a bad rap. Just my 200 cents.