The reasons, from what I can tell, are as coherent as they ever are in Star Trek. The subtext of that statement, however, is that you believe you could have done better.Sometimes you need the occasional contrivance to keep things moving. ST09 had them just for the sake of having them, and to avoid actually having to come up with an even halfway coherent reason for something happening.
Considering the original pilot of Star Trek saw Christopher Pike trapped in a medieval dungeon fighting a sword-wielding kinda-supposed-to-be-an-ape-man, I should say that impression is far from inaccurate. You should also be aware that the Rura Penthe scene was envisioned largely as an excuse to showcase exotic/modernized versions of TOS creatures like the Salt Vampire and the Gorn.Regardless of just how inaccurate that impression was?
Strongly disagree. Science fiction strays in the realm of "impossible" all the time, and Star Trek, especially so. Where they get into trouble is more along the lines of the "conveniently possible," where you need a solution to a problem so you make one up off the top of your head and expect the audience to believe this was a possibility all along.One of Ted Sturgeon's laws is, "Never ask your audience to believe more than one impossible thing at at time." Where Star Trek generally got into trouble is when they violated that rule.
STXI's violation in this regard is the "jettison the warp core" thing to escape the black hole. IMO it was the single weakest aspect of the entire film, though I find it excuseable because it was executed nicely and with a proper dose of high tension.
OTOH, warp drive is impossible; the audience believes it. Transporters are impossible; the audience believes it. Aliens that look like humans are impossible; the audience believes it. Ray guns that render people unconscious only are impossible; the audience believes it. Artificial black holes are impossible; the audience believes it. So all respect to Ted Sturgeon, but unless you can cite a more concrete example of "impossibility and improbability" that the audiences didn't buy, I think your problem is with Star Trek in general, not STXI.