The Clone Wars references the prequels broke were generally fixable.
A lot of discontinuities are fixable, but that doesn't change the fact that they chose not to be bound by what earlier books had established.
And The Clone Wars wasn't very good - I quit watching long before they introduced their version of Mandalore, so the books are all I have.
But we're not talking about one person's subjective experience, we're talking about the awareness of the fanbase as a whole. The fact is that it ran for five years and made a significant impact on Star Wars
canon, that it's come to be very well regarded by a large segment of the fanbase (you missed a lot of improvement by giving up early, though you also missed a lot of not-so-improved stuff), and that its overwriting of the novels' version of Mandalore was a prominent event that got a lot of publicity in fandom. Granted, an animated TV series wouldn't get as much publicity as a new live-action movie, due to our society's lingering, very stupid prejudices against animation as a medium (TCW was generally far more intelligent and sophisticated than the prequel films, and certainly a damn sight better acted), but that doesn't change the fact that fans who assume that EU continuity has never been overwritten before are drawing an erroneous conclusion out of ignorance.
I don't think it's so much "surprised" as "disappointed". I can understand why they don't want to be beholden to the details, but adhering to at least the broad strokes would've been nice, leaving open the possibility of fixing things to match.
Well, who's to say they won't? The prequels and TCW have drawn on EU characters, worlds, and concepts when it suited them -- the name Coruscant, characters like Aayla Secura and Quinlan Vos -- and overwritten EU continuity when it interfered with their plans. Presumably the same will be true here. It makes no more sense to assume that everything will be thrown out completely than it does to assume that everything will be slavishly adhered to. Naturally the needs of the new films themselves will take priority. If it serves the films to use an idea from the EU, it will be used. If it serves the films to ignore an idea from the EU, it will be ignored. That is the way it has pretty much always worked, both in SW and beyond.
Not only is Abrams a much bigger SW fan than he was an ST fan, but his ST movies do draw on ideas from the novels. The names of Kirk's parents were introduced by Vonda McIntyre, while Uhura's first name was coined by William Rotsler and adopted by many novel and comic authors. Uhura's portrayal as an expert linguist is an approach the novels have often taken. And the film's version of Kirk's maturation arguably owes something to Diane Carey's in Best Destiny
(which screenwriters Kurtzman & Orci have cited as one of their favorites).
I think a lot of people are jumping to the conclusion that just because Abrams and his collaborators chose to create an alternate timeline for ST, that means their goal is to throw continuity out the window for SW. That's a completely illogical assumption, because the situations are entirely different. In the case of ST, the goal was to go back to the familiar TOS characters, since they'd always been the most popular and were the best option for successfully drawing in a new audience, and tell new, updated stories about them. The best approach to suit that particular goal was to start a distinct continuity, one that wouldn't be limited by all we knew about the future of Kirk and his crew. They didn't arbitrarily "throw out" past continuity because they were big meanies who wanted to trample on our childhoods; they made the choice that best served the needs of the particular assignment they'd taken on. But this is a different situation, a straight-up sequel set a generation after prior canon films. Sure, they're likely to take its own path and not be restricted by the novels' and comics' ideas about that era, but that doesn't mean they'll just arbitrarily reject everything out of sheer cussedness. They may well choose to incorporate or pay tribute to certain characters or ideas from the EU, insofar as they're able to do in the context of the story they choose to tell.