Fix Beyond by adding two TOS tropes. 1) Instead of the Enterprise answering the Altamid distress call, have them be sent out to find out what became of the ship that did - something TOS often wound up doing. 2) Instead of destroying the Enterprise, have them find said other ship destroyed. While an away team beams/shuttles to the surface to look for survivors (again, something which was done a lot in TOS), the Enterprise winds up in a firefight against the swarm, able to beat them back for a while. Eventually, Enterprise and Franklin (crewed by away team) get together to fight off the swarm and Krall. As for 2009? It's said in TOS that Kirk taught at the Academy. So, here's Kirk, a few years after grad, unsatisfied, not getting anywhere in his quest to explore space/become a captain, etc. He's a professor teaching kids younger than him that get to live out his dream, the one PIke promised, while he's only been on a couple of shakedown cruises at most. The only satisfaction he gets is an academic rivalry with Spock. So when the Vulcan comes out with his new "no-win scenario" simulation, prof Kirk decides to make a fool out of him. When the Nero crisis begins, and it's all hands on deck, Kirk sees his big chance to get out into space and prove he's good for more than grading papers. Heck, fix Into Darkness too. Post-Nero, assuming '09 plays out as it actually did (Cadet Kirk) Kirk loses the Enterprise back to a recuperated Pike and finishes his education, then winds up on Enterprise as first officer somehow (maybe PIke's original FO is transferring, or sick).