Apples to Orange Catholic Bibles: Batman has always supported a plethora of interpretations and continua, Star Trek--not counting parallel universes--only one. No one is asking us to view Batman Begins as a prequel to the Batman tv show. From what we're getting on Star Trek (XI), we are meant to see it as a prequel to the Star Trek tv show of the sixties--the presence of Nimoy seems to cinch that. So it is a bit more problemattic.
I say "seems" because (to bring in a third series) the Craig Bond films have Judy Dench, playing an alternate version of the M she played in the Brosnan films, so there is a precedent for a total re-boot carrying over vestiges from the last iteration in ambiguous ways. Old Spock may be played by Leonard Nimoy but he may not be the same Spock we saw in the original 79 episodes any more than Craig's Bond is Brosnan's Bond or Bale's Bruce Wayne is Adam West's.
I find that the less I "care" about this, the more interesting it becomes as an intellectual exercise. I care very little about Bond films and thus I've enjoyed most of the old movies, all the Brosnans and Casino Royale and I'm looking forward to Quantum of Solace. I care very little about Batman and thus I hated Burton's first one and both Schumachers on their merits (I do like Batman Returns). I thought that Batman Begins was criminally overrated and liked Dark Knight but with some rather major caveats.
I'm looking forward to judging Star Trek on its merits as well. The only way I can do that is by not being a fan. And that's fine--Trek hasn't been good enough to warrant fannish devotion since I was twelve years old. These last 26 years I've been going on force of habit.