Part of me wonders what it is about the prime universe that attracts some people so much that JJTrek cannot have. The only thing that I can think of is that Vulcan is destroyed. But that's a good opportunity for stories. Or maybe some think that because of all the changes in the timeline, it's unrealistic to expect their favorite next gen characters to exist. It could be, but unrealism isn't going to stop those in charge of this particular universe. Or is it just that they want to see what happens after Nemesis or the Dominion War and are afraid that Trek will seemingly continue to just reboot Kirk/Spock? Or is it really the production style of the old shows that draws them in?
Speaking for myself, and I like both Classic and NuTrek, I think what attracts me most about the original continuity is simply that there's a huge fictional universe that I've come to know and be comfortable with as a place to escape when watching TV or reading a book. We all know the characters, the places, and technologies, and it's natural to want to continue visiting it, in my opinion. I like to see where a character that I've known for years and years can be taken by good writers and also seeing where lesser known characters that were interesting but were only on the show for a short time. Set against the back drop of this familiar, comfortable, and second home that writers have been building for 50 years, I think it makes the characters more relatable because I can empathize with the character and story on two levels -- what it means to me in the real world, and what it means for the character in his or her world.
I'm happy that the prime universe continues in the novels and enjoy the fact that the modern novelverse, at least as far as I've been able to ascertain, has a consistency at least as good as the prior incarnations of Trek on TV or movie screens, and extends that continuity. Like I said above, it's a familiar place with characters we love being put into another situation that we enjoy watching them figure out.
The question to me really isn't if I want the prime timeline back, because as far as I'm concerned, it's still there, just not on the TV or movie screen. It's a trade off though -- yeah it's sad there's not anything new in the prime timeline on a screen with special effects, actors, and the like, but at the same time the book lasts longer and what I imagine in my head while reading is always going to be more realistic and impressive looking than TV
and the writing is, for the most part, better than Trek became in the later years (I still give DS9 a pass though because it was written well IMO -- for the most part).
NuTrek just hasn't been around long enough and I simply don't care about these versions of the characters as much, or about the circumstances of their timeline. That's not bad though, and it doesn't mean I don't like the characters or the world they're in. I like the characters a lot and enjoy watching them. It's just math. I've known the prime timeline my whole life and I just met these guys, so I'm always going to enjoy visiting the prime timeline, because it's still being written and I'm used to it. NuTrek is just a bonus on top of that because now I get to see how the same characters and situations develop in a different "quantum reality."
As far as the canon, I really can't think of any time between TOS and VOY where the canon really had a negative impact on the stories. If canon was a problem, they ignored it plenty of times and still told a good story. As was said earlier, I think the production and writing just got stale and, IMO, still had a somewhat 80s television sensibility well into the 2000s. That type of Trek was going to get cancelled, canon or not, prime or not. I think the novelverse shows that you can stick within the same timeline and write really good, compelling stories.