The only flaw I can't get over is the complete r*pe of the Koybyashi Maru incident. They turned one of Kirks coolest moments intoa childish prank.
This I can get over, since the paths had already diverged. The real Kirk did it much cooler, but this is just the fake Kirk
Anyway here is what they should have done :
Red matter :
Alien artifact, catalyst which removes the repulsion between matter, red matter separated from the main mass loses it's properties in minutes, requires matter of either sufficient energy or sufficient density to cause a sustained chain reaction (this can be true even if the movie doesn't come out and say it, but as long as Spock is mind melding he could do a little exposition making the stuff a little more believable).
Reason for Romulans to hate Spock as much as they did :
Spock went to stop the supernova, Romulus destruction was an unforeseen side effect ... Romulans initially believe he sacrificed their planet to save his own, after learning the truth (Spock interrogation) they just rationalize their lust for revenge regardless.
Reason for Romulans able to drill into Vulcan unopposed :
There's a desperate fight somewhere, entire starfleet is gone, he used the parasite to get Spock to tell him the way to hack the static planetary defenses of Vulcan as well (also introduce some scenes where the operators of the defense grids desperately try to prevent the hacking and failing). They also faked transmissions from Vulcan to the fleet to make it look like they were okay, the distress call to earth was from a lone message pod which managed to get through while all others got destroyed.
Transwarp teleportation :
SCRAP IT, make the Enterprise still be in orbit making repairs.
Spock and Kirk meeting in cave :
Kirk mentions "what are the odds" Spock makes up technobabble explanation that the universe seems to be trying to pull itself back together, creating highly unlikely accidents moving the present back closer to the way it was.
There, that wasn't so difficult now was it? Fucking JJ Abrams too used to plotholes from Lost ... unfortunately most Trekkies seem to be lapping that shit up as much as the Lost fans.
After the reviews of Transformers 1 and this Movie I'm feeling like most sci-fi fans in the world have no standards left ... if the effects are good and at least half the scenes are decent it doesn't matter how much the rest of the movie sucks, it will still be called a masterpiece. Have some standards people, there is no excuse for the plotholes ... it's an even mix between decent and dime level writing in a movie costing hundreds of millions of dollars, JJ Abrams should be flogged for each and every one of the huge screw ups. How can this level of amateurism be accepted in writing and little else? The actors did their job (as good as possible, no actor could have made the elevator scene or the cheery "blow em up boys" ending believable) the writers failed.