Ok here we go:-
1 There was a lot of character stuff,Spock/Uhura argument, Kirk losing his mentor and father figure and having to grow from that.
2 Kirk was a rulebreaker in TOS, but in this timeline though, he's been promoted too fast and is too arrogant. Yes in TOS he was almost always proven right, but at this point in the new timeline he hasn't earned that, he's just a hothead who ignores rules that do not apply to him. By the end of the movie, he's more tempered.
3 Basically, you're saying Spock shouldn't care because he's only had Kirk as his Commanding Officer and friend for a year?
4 Scotty got more to do this movie rather than being "just gone", Sulu had a period in the spotlight last time, Chekov was still used this time, McCoy has never been the "referee" between Kirk and Spock, so not sure what you were expecting his role to be here.
5 Scotty is responsible for the safety of the ship, and therefore responsible for the ordnance. he doesn't think it's safe, he doesn't have to accept them, period. Arguing that "Romulan ships" or "being underwater" is the same as "72 great big explosive devices stored inside the ship" are the same is, well, odd.
6 I guess you missed the whole reason that Carol Marcus was around was that the Section 31 doctored info on the torpedoes did not pass muster? Also, are you assuming that Starfleet Regs means that Scotty is not allowed to resign?
7 Uhura TRIES and fails, that's the point. They didn't go in all-guns blazing, it was the last resort. I guess it would have been a better sequence if she'd succeeded then Khan just turned up and surrendered.
8 And the battering that characters have taken in past shows and movies are effectively ignored - nothing new there.
9 They may have lived or died it isn't clear - but why would the fact that he claimed earlier in the film he hadn't lost a crewmember make a difference to him losing them now? Is he infallible, or did he just not run a memorial service while he was busy with all the other life-threatening events going on? Remember all those end moments when the bridge crew are laughing and joking at the end of TOS? Yeah, a shame the M5 just killed 430 people, but yeah still the joke was funny.
10 Already been done to death that an exact replica or design of a TOS ship/sets/uniforms would look dated now - it was also never stated anywhere on screen that the wrecked moon was Praxis. Even if it is, has been a new timeline since Kirk's birth, so the Klingons may have overmined the moon earlier.
11 If McGivers hadn't changed her mind, Kirk and probably most of the bridge crew would be dead, and Khan would have been running around the galaxy in the Federations most powerful ship. Nope, he don't sound dangerous at all!
12 Prime Directive has never been consistent. I think in this case Spock was ok as long as they weren't actually seen, being able to save the planet without leaving a "footprint".
13 So, Marcus crewed his ship with loyal members of Section 31, and you're concerned they were going to follow his orders? They wouldn't be on his ship if they weren't going to. As to Kirk transmitting through his ship, he wanted his crew to know the truth of what was going on, if they survived it would be his word against Marcus - having a few hundred witnesses to the conversation would always help!
14 You can't really argue that Section 31 is incompetent because of one security guard who doesn't do his job. By that token, because the security guards were overwhelmed by some miners on Janus IV, therefore the Enterprise crew are all incompetent.
15 We don't know what kind of co-ordinate system the Federation uses, it could be sector, grid, subgrid for all we know.
16 And had Khan acted any other way then in his character (i.e. genetically-engineered superior superman), then this board will be equally filled with rants that they changed Khan.
17 Wait, you have an issue with traffic management in the future? We have almost never seen ANYTHING about the future transport system, except for the fact that when Kirk was a kid you could still drive internal-combustion cars and when he was an adult he rode a motorcycle. Who's the say the swerving and breaking cars were NOT computer avoidance programs?
18 Why not? This isn't TNG with the replicators, there may be waste they cannot recycle at this time.
19 Oh, the old "Why is there no other ship?" argument, that has been done time, and time, and time again. "Only ship in the sector" "You're the only ship in range". Boring, but been the same since forever, will never change. As to the coming out of warp thing, we don't know what kind of effect could have occurred by the Vengeance and Enterprise being in such close proximity, or perhaps Sulu got distracted by all those phaser shots tearing into the ship.
20 Khan waited for the right moment to attack, the Klingons may be busy with wars/conflict elsewhere, the Vengeance only had a small crew, that was stated onscreen. A small crew means no security patrols on every single deck.
21 Kirk has no incentive to fire the torpedoes? Those were his orders from Marcus! He wasn't supposed to try to get Khan back, he was supposed to launch all the torps. Why 72? Because THOSE WERE HIS ORDERS. Marcus expected him to carry the orders out, then be stranded by the sabotaged engines to be destroyed by the Klingons. As to why have the Enterprise destroyed, it was precisely BECAUSE it was the Federation flagshhip, to cause more outrage at home.
22 It could be just as possible that transport beaming TO a location is fine, but transwarp beaming FROM a location isn't. As to contacting Scotty, well I can phone someone on the other side of the world with my mobile phone, and I don't have a 23rd-Centruy starship to boost the signal.
23 We don't know exactly what Khan's plan was, but at the meeting he wasn't planning on killing just Marcus, he was planning on killing every single high-ranking starfleet officer that could have been used to pursue him. He may have had some plan on Kronos, but that was changed when he was informed that the Enterprise was about to fire 72 torpedoes at him.
24 Marcus would assume that Khan was in the brig, so if he decided to try and get him that's where he would be. Kirk then lied saying Khan was in engineering, to give Marcus two places to look. Misdirection, plain and simple, what's the problem? As to Space Seed, Khan had absolutely every intention of taking over the Enterprise the moment he gained consciousness - he was already studying everything he could about the ship before he knew his identity was discovered.
25 And exactly what would have happened had Carol Marcus been off the ship? Oh yeah, they would not have opened the torpedoes, and Admiral Marcus would have trashed the Enterprise without a 2nd thought. I'm glad she wasn't important.
26 Distraction AGAIN (or did you miss the Captain Chekov sequence in Star Trek V?). Kirk knew that Khan would assume someone was after them, so tried to indicate the Enterprise was just going to wait for him to surrender before attacking.
27 It wasn't fixing, it was re-aligning something that had become loose, something that may have required engineering crews with heavy tools to move.
28 We've only seen transwarp beaming send two people at once. Bit difficult to launch an invasion like that. As said earlier, we also don't know if beaming back via transwarp beaming works, so if things go wrong, you can't get your troops home.
29 They'll fly and target, but the warhead isn't very powerful. As he's only intending to killl the occupents anyway, that doesn't matter much.
30 And McCoy knows the blood of just any augment will work exactly the same as Khan's blood how???
31 Can't lock onto a constantly moving and weaving Khan, but can onto a transport that's moving in a straight line at a steady speed. Can't see a problem with that. And then if you got planetside transporters trying to lock onto Khan you got the same problem (weaving, running) except of course the added line-of-sight issue. As to calling someone, a big freaking starship just crashed into San Francisco, I'm pretty sure there'd be a few busy lines.
ALL your points on spot on. The character development was pathetic at best. The meritocracy of the federation is gone and has been replaced by childish cronyism and whining.
The daring of kirk is condemned and the effetness of go along to get along is rewarded.
Just because this poorly written movie bears the name of star trek does not give it a free pass to criticism.
If Bad Robot Trek is dead, then there will be no more Star Trek. 
