Different franchises have different pretenses, creating different expectations in the audience. This is why cross-franchise comparisons don't always work in these discussions...
Stories about Batman can be told in multiple media (and multiple actors can play Batman in the same medium), and they're set up as distinct takes on Batman's life; while stories about someone like Indiana Jones can be told in multiple media (and multiple actors have played him), but they're set up as stories from different points in the life of the same Indiana Jones.
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Like Steve, I find it "reasonable" that readers/viewers expect stories to connect when they share elements of their "fictional reality" in common and aren't explicitly told that there's an alternate timeline at work--even if it's possible to retroactively argue in favour of such "branching."
Here it is, what I wanted to say but didn't quite know that I wanted to say it.
It is admittedly a perception issue. I guess it goes back all the way to the early novels. If I'm not mistaken they started in the early 70's and were quite plainly meant as the further adventures of Kirk and crew. I even remember reading something not too long ago with one of the authors from back then who had "killed" off Kirk and someone from the publisher or studio can't remember, was telling them they needed to "resurrect" Kirk for the upcoming movie!
If, like Batman or James Bond, there had already existed a precedent of reboots or re-imaginings, it would be easier to take. But the novels have always been sold (whether stated or not) as the further adventures of Kirk, Spock and the gang, and with their likenesses on the covers to boot. If they do a separate line of novels based on the new movie, and use the likenesses of Pine, Quinto, etc, then those can be accepted as a different "reality" than a novel with Shatner and Nimoy.
Yes, I know it's not that important and I should really just relax, but I also feel that there's a bit of a Caveat Venditor feeling that's in place, esp for such a promiment franchise. I'd also throw in a "I guess I just expected too much from you", but that's too passive agressive even for me

Just another fan of the Nice, Neat Box theory of franchises.