sovereign002I agree with the point that they are smart, even smart enough to escape a prison cel. Still there is a huge difference between this and knowing how to pilot a space ship. Perhaps they will learn if teached long enough. However they do not seem to have the physical qualifications to use most of the ships functions (e.g.: weapons, tactics, navigation) if you look at how the alien pressed the button to activate the 'ice spray' on the scientist who is in the cel you see it doesnt use its fingers, instead it uses its tongue. This shows that their fingers are not as developed as is required for controlling a ship. I assume most ships functions use smaller buttons than that of the 'ice spray' (which was a big red one) and that their tongue will therefor be to big.
One of the main reasons why the colony was overrun by aliens was because they did not have a armed military unit, if you only have some small weapons its no wonder you cant defeat multiple strong, fast and armoreded(exoskeleton) aliens. Besides this colony did not have a population in the hundreds, it had 200 max looking at the total size of the colony and the amount of buildings, infrastructure. Besides most of the sorounding area hadnt been decently explored yet, so people would not go ringing the big alarm when a couple of guys have dissapeared, they just think they got lost or something giving the aliens the time to organise and grow in numbers (assuming the first family didnt make it back to the colony in time). In our society im sure it would not go unnoticed when more than say 10-15 people disappear in the same area and in the same week so it would surtenly not in a much more advanced where you can start looking for biosigns, use comlinks,... The aliens would never have the change to reach more than 200 before the local police finds them (who are armed with handphasers: a decent weapon that can do medium damage and has a 'overload' funtion=grenade) The aliens in aliens 2 were able to be detected from close range but while still out of line of sight, im sure star treks advanced technology would detect them with much more ease. To cut things short the aliens wont be able to have eliminated 5000 people (and thats a very, very maximised number).
I don't think it's really an issue with spaceships and Aliens, since the Aliens are either going to stay planetbound, or just infect a ship, not try and have vast naval battles in space. I don't know much about Star Trek, so I don't know anything of internal ship defences, but I assume that if they're sending people groundside to fight the Aliens, the Aliens can also get into the ship, and I assume they wouldn't simply obliterate the planet and all it's inhabitants to destroy the aliens. Same goes for Star Wars.
I think the empire would just go, "Dude just fire already yaaaaaaaaaaaaa"-Palpatine Then that would be the end of it.