1) What was Nero doing for those 20+ years? I know that in a deleted scene they actually explain this, but in the theatrical it's never touched upon. Why is that?
2) Not a single member of Nero's crew realized just how insane everybody else has become and didn't object to galactic genocide? Even that piece of garbage Nemesis proved that there were Romulans who were horrified at such a concept, and that was only Earth as the target.
3) The entire concept of red matter.
4) One star exploding was a threat to the entire galaxy?
5) What the Hell ever happened to Kirk's mother? She's mentioned once after the whole opening and then she just vanishes.
7) For a race that's supposed to be about logic and conquering their emotions because they view them as causing nothing but problems, those Vulcans sure are bigots towards human hybrids. You know, the species that helped them FOUND THE FEDERATION and they've been working with for well over a century now.
8) Engineering... oh god, what did they do to you. You used to be my favorite part of any starship...