The film had a weak plot. Fortunately, we don't need to be professional screenwriters to perceive that this is so. There is actually remarkably little disagreement on the point anyway, the most common counter-arguments being "It does not matter" or "Trek has had weak plots in the past."
I'm also pretty confident that the writers and producers knew that the plot of the movie was contrived and full of holes, but decided to go with it anyway on a cost/benefit type of analysis. Chiefly, they must have decided that having Nimoy's Spock around was worth the time-travel contortions required to bring him into the story.
Ironically, one motivation for this was probably to please longtime fans, some of whom seem to be among those most displeased with the contorted plot. Whatever. They thought it was worth it. That's what we have.
I can think of a few ways to smooth over some of the glaring coincidences surrounding the Delta Vega sequences, but I confess I am at a loss when it comes to thinking of a more elegant way to bring Spock Prime back in time. This was going to be contrived if it was going to be done at all.
For me the lingering question is whether having Nimoy around was worth it. I think a straight-forward reboot might have made for an even better movie, and I think it would probably have been just as successful, if not moreso, since I don't think Nimoy's presence has been a major factor in the film's success at the box office. Such a movie would almost certainly have had a simpler, more satisfying plot.