From my experience I know that Ciri is certainly a controversial character and among Saga fans you can easily find both people fond and not fond of her, if not downright hating on her. I can assure you that this kind of thing will carry on to the game and for sure she will get as much new fans as a new detractors. Major reason for that is not if Ciri is MS or not, but if The Witcher 3 story will be swallowed (heh heh) by her. The answer to that is yes, it will be. Why? Well, the posts praising Ciri above explained that really well, but instead of easing up some of the critical arguments, they ironically somewhat provided even more credence to them. Ciri became a fabric of entire Saga, she became main female protagonist, all Geralt's goals revolved around her, she plays a key role in plans of almost every villain and major political player, gains a new powers as plot demands. She basically turn it into Ciri Saga, while Geralt ends up as a supporting protagonist. After all of that do you even have any doubts that the main storyline will strongly focus on her?
Just like Raiden in Metal Gear Solid 2 was hated for replacing Snake, Ciri gained a mixed responses because she took a lot of pagetime from Geralt. Let's face it, we got into this story while reading about Geralt's various adventures, so when the novels started more and more focus on this one girl who previously appeared only in two last short stories, you can see why many didn't find her to be a good alternative. Now people are worried that the same thing will happen in a game, even if you going to play as Geralt. The fear increases even further, as it was promised to us as end of Geralt's Saga, so some people are naturally afraid that focus on Ciri will overshadow conclusion of Geralt's own story. While I'm sure that Ciri will be a huge part of The Wild Hunt storyline, I believe that CDPRed will deliver what they promised and we all will at least shed a tear after watching final scene with Geralt.
Now as I said before, Ciri will get a new fans and detractors who will judge her without knowing the original novels. It will be a pretty crucial moment, as overall reception will decide if she's able to carry the franchise further on her own. I think she has her chance, as now stories about father/daughter type of relationship are really popular in video games. Clementine, Ellie and Elizabeth were not only a hearts of their respective games, but even manage to beat in terms of popularity their "fathers". If Geralt/Ciri relationship will be done equally as good I think that people will warm up to her pretty quickly.