In the original timeline, I haven't seen a federation starship other than USS Voyager on the surface of a planet, whether it was capable of landing or not.
In Star Trek Into Darkness,
it was displayed that Enterprise was kept underwater on a planet.
My Question:
What was the point of bringing Enterprise to the surface, which enabled a couple of chances for violation of the Prime Directive? Why couldn't observations be done with Enterprise in orbit?
After decades of technobabble accreting, the Star Trek universe is surprisingly resilient to plot holes. Technobabble is the gaffa tape of scriptwriting, it can fix and hold anything together. Here is an "in-universe" explanation for the submerging:
In the event of the volcano erupting with a lot of ash, the dust of a Nibiru volcano and its electrostatic potential would cause ionic interference (1) with the confinement beam, leading to deadly pattern degradation in the transporter signal. Communication with crew on the ground would likewise be hampered.
Note that in the movie, Spock is at some point in the volcano but unable to be beamed out, due to interference (2). This shows that we are dealing with a particulary bad volcano transporter-wise. Wouldn't want the crew on the surface and the Enterprise in space if the volcano erupts and the material causing the interference spreads to the atmosphere. (We can here assume that Nibiru already suffers from Trinimbic interference (3) .)
When quizzed, screenwriter and producer Roberto Orci came up with a similar explanation on the spot (2), only adding that it's magnetic interference, not Trinimbic. (Dumbing it down for the journalist no doubt ;-) As an extra precaution by the producers, Scotty is questioning Kirk's decision on submerging
The only reason I can think of for landing on the planet and hiding underwater is to allow for a stealthy approach by the crew, much like the way submarines have been used to insert agents into foreign countries in our own world.
Although, given the outcome, it was almost certainly a mistake, but it is possible for a chain of apparently sensible decisions to lead to a disaster.
The ISS is visible to the naked eye, and the JJPrise (at either stated scale) is vastly larger than the ISS. Ergo: An orbiting Enterprise would be quite visible to the inhabitants. So "hiding" under water (assuming you could get here undetected) is as good a solution for not interfering as anything. It's still stupid.
Given that they weren't allowed to interfere in any way and were supposed to passively observe the populace, I suspect Kirk needed additional cover for the mission to save the poor lot.
The act of submerging the spaceship is completely outrageous given existing canon and must be seen in the eyes of a rebooted canon.
Shuttles can also fly from space. Teleporters were not the plan anyway.
Honestly, hiding the ship underwater can only have been a "gut feeling" from our captain Kirk. In the end it saved Spock, so the feeling retains its magic.
I would like to add the following plausible reason for not staying in orbit.
If you take the size of the Enterprise to be about 300 metres, and if you want the ship to stay within transporter range, it cannot be farther away than 10'000 kilometres (taken from this answer here), then the Star Trek will cover a range of about 3E-5 radians or about 1 arc minute. At least for the naked human eye, it is small enough to not be perceived. But if you had trouble actually catching somebody with the transporter, you'd have to come a lot closer.
If we calculate backwards, the closest the Enterprise may come to the planet to avoid becoming visible with the naked eye are ~1500km)
They decided to go down to the planet to try and stop the race of beings on that planet from being destroyed by the volcano. It was easier to get the shuttle from the starship to the volcano from the planet surface rather than from orbit allowing them to plant the charge to stop the eruption from destroying the sentient species.
