If anything, I would have preferred them to save Chekov for the sequel. I know they wanted to showcase the 'Big 7' but, while I enjoyed the character, I would not have missed him if he'd been absent. New fans could not have missed him, and for the nerds, there is an obvious reason for him to be absent (he's too young at this point in time and Chekov wasn't around for at least the first year of the TOS mission (although he was on board, off camera at the time of Khan's incursion in Season 1, which was year 2)). I don't think any of us can say that the film itself would have sufffered if he'd been absent.
I know people say that they didn't know that there would be a sequel but I'm sure the same was true when they made the Batman movies but they didn't feel compelled to include Robin, just in case.
I would have preferred them to showcase Rand as a security guard instead of Chekov so that we could have had a second female crewman in a minor role and then feature a correctly aged Chekov in the sequel where there was a bit more time to introduce him. I'm ambivalent about the wunderkind element of his character, especially as TOS Chekov was actually a bit dense, but I didn't like the scene where Chekov was casually placed in charge of the bridge at a time of crisis.
BTW - Most of the others haven't had their ages changed. The problem is that if they promote them to be department heads with no prior experience it will strip some credibility from the characters. Being good at their jobs should lead to promotion eventually but is not the only reason for promotion (hopefully some time will lapse between the two movies to cover this). Plus Kirk is becoming a Captain only 3 years ahead of schedule but he is becoming Captain with 7 years less experience, no diplomatic credentials, and a tendency for risk-taking far beyond TOS Kirk. I watched 'the Hurt Locker' the other day and I was taken with the parallels between NuKirk and James, especially the different way the people around him reacted. NuTrek looks extremely childish by comparison. If I was in the lower decks I'd be really worried!