For what it's worth, I'm a huge Star Trek fan (my interest in watching it second only to Star Wars now, thanks to Harmy and Adywan, as I refuse to watch the SE's).
I've seen every episode of every (live action) series of Star Trek, many of them more than once. Granted, I'm a child of the TNG-era, and I don't like TOS much because of its campiness and over-acting. However, despite my not liking TOS, I do love most of the Kirk movies (2, 3, 4 and 6), having seen Star Trek IV in the theater when I was eight years old.
I liked Star Trek 2009 a lot.
The reason why JJ Abrams not initially being a Trek fan is a good thing, is because he's not intrinsically bound to the many constraints that the Trek universe had set for itself. I've seen the behind-the-scenes stuff for his Trek movie and he did seek a lot of input from various people, each of whom had different levels of interest in/knowledge about Trek (some of whom are serious die-hard fans).
Actually, the one thing I remember most about what JJ said Trek needed was that Star Trek is like classical music and Star Wars is like rock music; so he felt that Star Trek needed some "rock" injected into it in order for the franchise to capture new audiences. And you know... I agree with him about that. Star Trek, while awesome, had become so bound by its established canon, that it would have been difficult to continue the franchise with the intention of gaining new fans without rebooting it and/or finding a new and different approach for it to take.
It's perfectly fine for people to prefer the "Prime Universe," but they still have 24 seasons and 10 movies to fall back on. The problem wasn't with pleasing hardcore fans, it's with gaining new ones--which is the opposite of Star Wars' problem as I see it.