By all means, the connection between the Baron's wife and the Crones and her tragedy was done right, it is anything else in the Crones quest that was done wrong.
1. The fact that the build-up and exposition to the Tree Spirit was done through a completely optional and such small mean is bad. Why? Because when all the other important events in the story have a straightforward and clear build-up then it makes the Spirit "build-up" (I have a hard time even using this term here) inconsistent and therefore bad.
2. Okay, if the kids always lived in the swamp and the Ladies eat them and all is well (in a very twisted kind of way to be sure), why then would the Crones need Anna to foster the children? Everything was fine before she came, how exactly does she "serve" the Ladies now? This is a plot-hole
3. As said, this I agree with
4. Did the Spirit told Anna to save the children? How come Anna know when do the Crones watch and when they don't? As it seems they exist in some different magical-metaphysical dimension whenever they want to. Where did the children go exactly? And that still doesn't answer my question, why couldn't Geralt save the children himself?
And that's only half of the problems with the Crones story.
I agree that the Bloody Baron is the highlight of TW3 story but I can't really agree it's a masterpiece
1. I agree with this. I read all the books in every game, so it wasn't a problem for me. Seemed like Dark Souls-type of storytelling - a story is discovered, often through reading, and if not to pay attention - hard to figure out what a hell is going on. I sort of like to discover obscure things in the plot, but it is not conventional, and people who do not read and put things together, do have a hard time to figure out what was happening and why. Probably, this part should have been a bit more clear.
2. Sure, they lived just fine without Anna. But for me it is not a plot-hole, but sort of a point. Anna is given a task pretty much useless for the Crones, but extremely cruel and taxing for her. I see it as a sort of punishment/insult, and only just because they could make her life miserable. The whole year the crones were going to rub Anna's face into what she bargained for, watching the kids being led away one by one to be eaten.
4. Here it is just my interpretation, the way I like to see it. The Spirit probably can watch the entire Velen. We know the Spirit can lure the villagers to their deaths, so it may be that she either knew, or even nudged Anna to take the children away as soon as crones are not watching.
Anna is in full understanding now of what is going on, and, by saving the children, she is trying to make amends. So when the Spirit distracts the crones, Anna saves the kids, knowing full well that she will pay with her life. Where they are exactly - in other dimension, or some other part of Velen - I do not know, but if Geralt returns after conversation with the spirit, they all gone, Anna included. I don't see why Anna can't be with children at this point, given that she officially serves the crones. In any case, the crones blame her, and she dies whether a curse is removed or not.
Geralt can't save them because they are not there anymore.
It is the best plot-line for me because it involves a lot of difficult issues. Philip and Anna are surprisingly good people, who are genuinely kind and caring, but they both are deeply troubled and damaged by war and cruelty. Their inability to come to terms with their family issues, an unending cycle of psychological abuse by Anna/physical abuse by Philip, when combined with deeply evil supernatural reality of Velen, leads to a frigging nightmare, when both of their children turn into monsters (one - figuratively, into a witch-hunter, another - literally, into a botchling), and make Anna responsible for child sacrifices of the most horrible kind. No wonder that the conclusion is either totally horrible, or pretty depressing.
By the way, the best cut-scene for me in the whole game is when Anna leads Geralt to the chapel, and in place of an altar they see a picture of three beautiful ladies. The feeling I get is pretty freaky, and it is obvious that something is terribly wrong here.