As with my most common complaint about the Star Wars EU (which I have unfortunately been acquainted with): CHARACTERS! The MAIN ones. Focus on them and their journeys like the movies do. It's absolutely painful if you're a fan of the main trio of Luke, Han and Leia and care somewhat for Chewie and Lando. Hardly any of the EU material even notices those characters as the leads. Original characters, random Jedi and random pilots just don't do it for me.
A lot of EU garbage is hurt because the writers are more focused on coming up with some silly sci-fi/fantasy plot and not about developing the characters.
One thing that this movie did for the Star Trek franchise was bring it back to the core characters and their internal conflicts and personal journeys. If you want new Trekkies that were introduced with this film to care about the comics or novels, you've got to give the same kind of dramatic treatment that focuses on these characters. Sure, you can have a sci-fi plot-of-the-week sort of deal, but that's only interesting if it affects any of the characters on a personal level in some sort of way.
Now, a good idea for the Trek books/comics would be to maybe do some kind of origins series about each of the main characters: their youth, what made them who they are, their time at Starfleet Academy, etc...
It would be an excellent chance to try to tell the story of how Spock/Uhura came about (this would at least get some females to perhaps check out the expanded universe material--it's certainly the fanfic topic that's taken off), about Spock's first experiences on joining the Academy on Earth before becoming a professor or perhaps a bit with Kirk and McCoy's friendship at the Academy, Kirk's changed parental figures growing up, etc... It would also give a chance for characters like McCoy, Uhura, Scotty, Chekov and Sulu to get backstories that probably won't ever be told on screen.
Actually, if there's any topic that would be worthy of a new book series, it would be about each of the characters at Starfleet Academy. A fill-in-the-blanks series, if you will.