I disagree. Times have changed since the original series. Many of the following Trek series (TNG, DS9, and VOY) followed an ensemble format, more or less, throughout their runs. ENT, which tried to emulate TOS with a trio focus, didn't turn out so well. I think modern audiences would be more receptive to an ensemble film, especially in light of successful ensemble pieces like The Avengers and Fast & The Furious.
Plus ensembles would give every character-specific subset of fans something to enjoy in a Trek film.
Have times changed or perhaps the trio they use in ENT was just not done well?
I don't really think ensemble or trios or duos are more popular, I just think it all depends on the writing and the character chemistry.
Anyways in these new films Kirk/Spock are still definitely the main characters. Yes there is somewhat of an ensemble feel but this isn't like Game of Thrones where it would be hard to say who are the main characters.