So I doubt after so many days that I'd be able to do a decent job on Star Trek Into Darkness. However, it would better fit the original purpose of this thread, as I really enjoyed the film immensely, and this thread is for critiquing films I enjoy in jest. Your enjoyment of the film is irrelevant. Only my enjoyment matters. ;)
In all seriousness, one flaw stood out to me right away: transporters! Why is it that Kirk can transport from Delta Vega to the Enterprise at warp speed using Scotty's transwarp principle, and that same principle is used to transport...erm...John Harrison to Kronos many lightyears away (bearing in mind that planets are rotating and oribiting at thousands of miles an hour in solar systems that are orbiting the galaxy), and yet it was impossible to beam Spock and Harrison off of a moving vehicle, because in this alternate timeline transporters can't lock on moving targets from even relatively close distances? Maybe one could say such was an acceptable excuse for Spock's mother's death in the first film, but by now Scotty's technology should have at least included a modest upgrade to most transporters so they could at least lock on targets not moving too quickly.
JEDIT: Feel free to create your own contributions to the STID critique list.