it's an enjoyable popcorn flick, but way too many plotholes and inconsistencies throughout (see Plinket's review of ST9 for more info)
1) EVERYONE is a freakin' genius. Ohura can speak multiple alien languages (including Klingon... how? Has the Federation at this point ever had any face to face encounters with the Klingons?) Ohura in TOS couldn't even speak Klingon; she had to use a book in ST5.
And Young little Chekov (17 years old in ST9), is not only a bridge officer but transporter guru (in BOTH movies) AND has learned how to run the Warp Drive by "shadowing Scotty" (per Kirk).
And McCoy is a general internist/surgeon/zoologist/hematologist?
2) You have a high level security meeting with all of your top brass.... at the top of a skyscraper, with exposed windows? And they certainly weren't transparent aluminum. Why not convene in some deep, hardened military bunker somewhere?
3) Khan can take out a squad of Klingons (who have redundant physiological aspects, per TNG), and then proceed to pummel Kirk, who doesn't die from the beating alone? Is Kirk stronger than a Klingon? (same goes for Spock)
4) Khan survives a starship crash from space... without wearing any type of restraint system... and LITERALLY WALKS AWAY from the wreckage.
Superman or not, he is still human, and his body would be goo.
5) You re-freeze Khan, after he has now killed a few thousand people (most San Franciscans). Why? Even if there is no death penalty in the 23rd century, there is still a justice system, and Demolition Man this ain't.
6) Spock and Khan fight, on moving transport ships, and jump from one to the other, without even a scratch. Literally, no blood. One punch/kick from Khan would be enough to know Spock completely off. See number 4.
7) Marcus forces Khan to help him design military weapons. Khan, with only 20th century technical knowledge. Of course, he has superior intellect, and I'm sure Marcus gave him white papers, but... really? It would be the equivalent of me asking Sir Isaac Newton to help with Unified Field Theory, after some input on the Higgs-Boson particle detector in Sweden.
8) The Enterprise engine core... has NO AUTOMATED SYSTEM FOR REALIGNMENT? No drones/robots/droids/remote control accessory arms in the case of a catastrophe? In the 23rd century, there would be NO RADIATION SUITS just outside the warp core reactor, so that you dress up before you walked in for repairs?
9) By the way.... that is some funky radiation that kills Kirk. Intense direct radiation exposure can cause neurologic and cardiac/respiratory injury that drops you dead. The human body wouldn't "hang on" for a few minutes, able to crawl around, breathe and speak, and then.... gasp... last breath... die. At least in TWOK, Spock's skin was damaged from the exposure. Here, Kirk merely had a few scrapes and his perfect hair. For example, the Japanese atomic bomb survivors were quite some distance away, but anyone closer than that (but not close enough to be instantly vaporized) most likely had sudden, agonizing deaths.
10) It's a movie, I know. A "technically" correct film that addresses every single little issue can be quite boring, and that's not the point. But, there should still be some inherent logic, within the movie itself, that is adhered to.