Not maintaining a human presence on the Sulaco (the marines' only interstellar transport (of huge dollar value)) is, in my honest opinion, what you might call a 'plot hole'. But a necessary and forgivable one, I think.
If you take a step back from the movie itself and think of James Cameron writing the script, he has often in interviews stated the importance of creating suspense. He does this right from the point that Ripley agrees to return to LV426. She knows and we the audience know that there is likely to be trouble ahead. From there on the level of suspense only grows more overwhelming - that's why Aliens is such an immersive experience. You have to watch right to the end before a level of safety/equilibrium is restored to the lives of the main characters - the ones we've learned to care about.
Anyway, back to the Sulaco being left unmanned. If there were crew present on the mothership, which in real life would always be the case (no matter the level of automation), then the marines on the planet below would have a potentially quick and painless way to escape their pressure cooker of a situation.
Let's say for argument's sake that the Sulaco was controlled by a powerful AI (as the Nostromo is in Alien) then surely it would be monitoring the activity at the colony site below? Not only that but it might conceivably compute in a microsecond the action it needed to take to save the marines i.e. send the second dropship down?
If there was a caretaker crew left on the Sulaco, then they could send the second dropship to the surface. This would have significant consequences for the logical flow of story events. Bishop would not need to make his constricted crawl along the service pipe. And, crucially, there would be no descent into the hell of the alien hive for Ripley, and no splendid finale face off with the dreadful queen.
So, as I said earlier, it's all about maintaining a level of suspense, i think. By eliminating the easy solutions one by one, the marines are left in an ever more precarious scenario.
Just my opinion, but happy to contribute my thoughts.