I didn't want to hate it. I wanted to enjoy it. Who goes into a theater wanting to hate what they're about to see? Other than a professional reviewer?
Just because you don't agree with the criticism, don't try to paint those who hold a different opinion as somehow biased and thus their criticisms invalid. Transporters in Trek2 only worked and only failed when it conveniently served the plot. It was one of many signs of EXTREMELY sloppy writing.
And the fact that other movies have plot holes, some of them excused by various people, is not a meaningful rebuttal. Reviews are subjective and thus not bound by objective criteria like consistency. I love me a good, bad zombie movie... that doesn't make any criticism I'd make of a bad good zombie movie invalid.
If you want further proof of just how stupid this movie is, enjoy:
http://io9.com/star-trek-into-darkness-the-spoiler-faq-508927844
I see this movie getting a lot more criticism for sloppy writing than just about any other Hollywood blockbuster with similar sloppy writing. Yes, I read that article and the writer starts off with a bit of a flawed premise. Kirk steals the scroll to get the primitives out of the temple so that Spock and company can get to the volcano unseen. It wasn't about getting them away from the killer volcano. The cold fusion bomb comment is just really nitpicky. The average viewer isn't going to know what cold fusion is other than a buzz word about energy generation. I think the term was used just to sound "sciencey".
As for the Enterprise under water, the merits of that analysis are debatable. While the vessel was built for the vacuum of space, we don't really know the structural specs of the ship. On Voyager, they landed the ship on a planet. I would think the ship would be subject to some strong stresses from an atmospheric landing. The ship is also designed to fly faster than the speed of light. Since that is impossible by today's standards, one really can't calculate the stresses involved with warp travel, thus it may be entirely feasible for the Enterprise to be under water due to the structural requirements to withstand warp travel. At 500 feet of depth in salt water, the pressure would be somewhere in the neighborhood of 300 psig. At that depth, it would make the swimming into the ship impossible so either it wasn't that deep or Kirk and McCoy should be crushed. Really, they shouldn't have survived the cliff jump at the height it appeared to be from.
The Khan criticism if legitimate, but that was more a casting choice than anything. They essentially ignored his back story and I don't think they even mentioned the Botany Bay. They certainly didn't mention his background of the Eugenics War. I would think they were more concerned about comparisons to the old Khan, however, the climax of the movie was written to draw comparison to Wrath of Khan. Not necessarily the character, but the plot. Really, they may have been better served by having Harison being another Botany Bay crew member that was either pretending to be Khan or attempting to revive Khan thus saving Khan for the next movie... which looks like they could be doing anyway.
While the writer is being tongue in cheek with a lot of his writing, he brings up a lot of "original universe character did this, and new universe character did this". They aren't the same people anymore after the universe changed. I believe I mentioned in several posts earlier that the entire crew is closer in age than they should be. Sulu, Uhura and Chekov should all be like 15 to 20 years younger than Kirk, Scotty and McCoy, but that doesn't appear to be the case here.
The secret branch of Starfleet, Section 31, was something that was created for DS9 and later used in Star Trek Enterprise. It isn't out of the realm of possibility for it to exist here. It also really isn't a stretch to believe there is a militant wing of Starfleet due to Nero's actions in the previous movie.