It all depends on how the game is 'designed'. Most MMORPGs have designed their games with single-player RPGs too much in mind. Every player is supposed to feel as if they could eventually rule the universe if only they were able to 1) kill enough 2) collect enough crap, and 3) recruit enough gang members.
Well that works well for hack-n-slash games, and settings where individual power (ability to destroy) is a virtue. Star Trek is not that kind of setting, and the designers must be well warned that the game will be a disaster if they do not create a maze which leads the mice toward higher goals/ideals. Instead of feeling you are able to be a master of the universe, you should feel that you are playing a crucial role inside of a structure that has a collective purpose, which depends on your faction.
Now, if you're a selfish, greedy, backstabbing, murderous, anti-social .. you get the picture .. of one variety or the other, you should be allowed to play a pirate/smuggler/spy etc., and be out for yourself alone. You should be able to slip through borders undetected, harass the fleet of this or that faction, and be a general nusiance / target.

.. loved by none, hunted by all.
Getting back to a rank system. If I am a member of a crew with a rank of Lieutenant, which everyone should be able to achieve in relatively short order, I should then be focused on gaining all the necessary skills, and complete all the required mission prerequisites in order to progress beyond that rank. This would be the same for similar ranks in the other empires of course.
A Lt. would be able to man any console on the bridge that they have the skills for. Perhaps they would not be able undock/dock the ship at a starbase, for example, something which should require a member of the command staff, the Captain or his/her 1st or 2nd officer.
When the Lt. meets the skill/mission/time requirements, they will be able to spend available experience points on the next rank. Now, as Lt.Commander they are able to fill the role of 2nd officer, 1st officer, or even as Captain, if again they meet specific requirements.
So, it is in fact a combination of rank and job title, which gives individual players access to specific ship capabilities which a person of lower rank without the specialization would not.
Now, it may not be hard coded that you have to listen to someone of greater rank, or who happens to be the head of your department or whatever .. but the fact is, you will have to, or the ship will not function. You will become a disruptinve nuisance to the crew, and perhaps one of the Captain's "special powers" will be the ability to eject you from the ship .. placing you back at the last base the ship had undocked from.