Probably PG-13. Hopefully an unrated version will be available on DVD/Bluray. Unfortunatly a R-Rating not only restricts the age of those that view a film but will also restrict the number of tickets sold. The studio will probably want to attract as many viewers as possible so PG-13 seems to be target rating for most films these days.
Personally I'd love to see excessive (realistic) violence and nudity in a Star Trek film but we will lucky if a character uses bad language. Spock's "Double Damn" and Data saying "S***T" were fun little moments for me. The pink Klingon blood was laughable.
The MPAA has weird rules and I have read that some words can only be used so many times in a PG-13 Film.