The aliens of Star Trek get a bit of grief for looking suspiciously like homo sapiens. I can tell he’s a different species because he has very slight ridges on his nose! She’s clearly an extraterrestrial because she’s got dots on her. And of course he’s an alien! His ears point up, and who would wear their hair like that???
So fine, it’s a fair cop. But let’s be fair, TV budgets are not limitless (particularly for shows for the relatively small nerd demographic), and I suspect audiences would have some trouble relating to, say, an amorphous blob or an intelligent jellyfish-type thing. I have always given Star Trek a pass because I know that a big reason the aliens that normally appear can’t be so alienating to viewers that they put too much of a burden on storytelling. Villainous or intentionally-bizarre creatures like the Crystalline Entity are of course the exception, in which they are alienating by design.
And really, Next Generation-era Klingons, Cardassians, Ferengi, and others, are really well designed, even if they are a little too humanoid for some.
Fortunately for Trek apologists like myself, there may be some sound justification for the franchise’s aliens looking a whole lot like human beings. George Dvorsky at io9 explores the idea that in order to achieve anything like a technology-wielding civilization, even an extraterrestrial species might do well — and indeed, may even need — to be very much like us.
First of all, they’d likely need to dwell on a planet’s surface; not swimming in the water, and not wafting about in the atmosphere (thus ruling out the whole intelligent jellyfish thing):
[It's] very unlikely, says [Fermilab physicist Don] Lincoln, that technically advanced civilizations like ours could have developed on a planet without land masses, like a so-called water world. He believes it's unlikely that intelligent dolphins will ever develop the technology for spaceflight. "There could be alien cavemen underwater," he says. "But truly, you can't smelt metal."
I'd say that's this is a) a point in favor of Trek-type aliens and b) a big let-down for believers in mer-people. All those metal tridents and whatnot? No way. Sorry, King Triton. You don't get to exist.
But here's the kicker, and it has to do with something called convergent evolution:
If [the alien species is] terrestrial, it would likely have to face the same sort of evolutionary pressures that our ancestors did. That doesn’t mean, of course, that all intelligent civs are descended from primates. But they may all take similar paths on their evolutionary journey, a well-documented phenomenon evolutionary biologists refer to as convergent evolution — those cases in which organisms not closely related independently acquire some characteristic or characteristics in common; mutation in evolution may be random, but selection is not.
Examples include physical traits that have evolved independently (e.g. the eye), ecological niches (e.g. pack predators), and even scientific and technological innovations (e.g. language, writing, mathematics, the domestication of plants and animals, and basic tools and weapons). Looking off-world, it’s not unreasonable to think about similar examples of convergent evolution; there may be certain ecological and sociological niches that are not Earth-specific or human-specific and are archetypal throughout the universe.
And only recently, of course, we learned from the Kepler spacecraft that there may be billions of Earth-like worlds in our own galaxy alone. And if they really are quite Earth-y, there's every reason to believe that their creatures might evolve to use brainpower and technology to dominate their environment. For that, they'll need things like grasping digits, limbs to carry them from place to place, light and sound-detecting organs, etcetera.
This is not to say they'd be bipedal with two eyes and ears (or speak English or be able to procreate with other alien species), differentiated from humans only by crazy skull protrusions , but it might mean that they would not seem quite as alien as we presume. They might even make for sympathetic characters in a space adventure story.