While Field Effect suits from TAS are considered a bit cheesy, would not something like that not be needed for planetary exploration?
In Spock's Brain, Kirk may mention "suit temperatures," but the line is unclear. If we wanted to press it, this could a live-action use of the "life support belts" of TAS, but, (like the deflector shields, which are not seen in TOS but are sometimes visible in TNG) the field is not visible in live action TOS.
It would have made far more sense for Spock to have beamed Kirk to the brig with an escort (Yeoman Rand step up please!) with the intention of using the base's communications array to get warnings out (the Enterprise's communications being damaged). Kirk meets Spock Prime on the base, learns about Nero and then Kirk has to use his command skills to persuade, through inspiration rather than insubordination, that he should be released so that this crucial info that the Enterprise needs badly reaches the ship. Since the ship's communications are down the only way is to transport.
Agreed that the script could have been better. I fancy that instead of the super duper transporter, the Enterprise was "slowed" due to its battle damage, and that Scotty had a souped up shuttle that could over take the limping Enterprise. Land in shuttlebay and get taken into custody, which avoids the comedic water tube ride and brewery tour high jinks. (Characters should be serious to reflect the danger and threats.) Scotty then helps fix the warp drive off screen then off they go at super warp speed. Same end result with same screen time.
Both these plans could have happened...if there had not been a writers strike during filming of the '09 movie, then maybe some of these jumps would have been worked out.
I don't hate the water pipe thing, though. I'm sure the "inert reactant" label is a joke, but I could imagine that it means this water (inert in the sense that no chemical reaction is taking palce) is actually "heavy" water containing deuterium ("reactant" in the matter-anti-mater reaction.) If they used water pies and tanks to store and move the deuterium around, that would make it easy and simple/safe to construct the ship, and actually then the brewery equipment would have some reason to exist...