Of course, there's an obvious non-diegetic reason for that. The aliens are played by human actors. Actors wanna act. Directors want actors to act. It's less fun if all of your dialog is synthesized by the sound department. But while it is an understandable and accepted trope, we shouldn't mistake it for representing a plausible reality.
First, aliens might not even use sound to communicate! Sound is a very good medium for communication--most macroscopic animals on Earth make use of it to some extent. But there are other options: electricity, signs, touch, light, color and patterning, chemicals. Obviously, a human actor will not, without assistance, be able to pronounce a language encoded in changing patterns of chromatophores in skin, nor would a creature that spoke that language have much hope of replicating human speech. But since sound is a good and common medium of communication, let's just consider aliens that do encode language in sound.
The argument was recently presented to me that aliens should be able to speak human languages, and vice-versa, due to convergent evolution. An intelligent tool-using species must have certain physical characteristics to gain intelligence and use tools, therefore... I, for one, don't buy the argument that this means humanoid aliens are likely to start with, but supposing we do: does being humanoid in shape imply having a human-like vocal tract, or a vocal tract capable of making human-like noises? I propose that it does not. For one thing, even our closest relatives, the various great apes, cannot reproduce our sounds, and we can only do poor approximations of theirs. Their mouths are different shapes, the throats are different shapes, they have different resonances and constriction points. We have attempted to teach apes sign languages not just because they lack the neurological control to produce the variety of speech sounds that we do, but also because the sounds they can produce aren't the right ones anyway. Other, less-closely-related animals have even more different vocal tracts, and there is no particular reason to think they would converge on a human-like sound producing apparatus if any of them evolved to be more externally human-like. We can safely assume that creatures from an entirely different planet would be even less similar to us in fine anatomic detail. So, Jake Sully should not be able to speak Na'vi in his human body, and should not be able to speak English in his avatar body--yet we see Na'vi speaking English and humans speaking Na'vi all the time in those movies.
And that's just considering creatures that make sounds in essentially the same way that we do: by using the lungs to force air through vibrating and resonant structures connected with the mouth and nose. Not all creatures that produce sound do so with their breath, and not all creatures that produce sound with their breath breathe through structures in their heads! Intriguingly, cetaceans and aliens from 40 Eridani produce sound by moving air through vibrating structures between internal reservoirs, rather than while inhaling or exhaling--they're using air moving through structures in their heads, but not breath!
Hissing cockroaches make noise by expelling air from their spiracles. Arguably, this should be the basis for Na'vi speech as well: nearly all of the other animals on Pandora breathe through holes in their chests, with no obvious connection between the mouth and lungs. They also generally have six limbs and multiple sets of eyes. Wouldn't it have been cooler to see humanoid aliens with those features, and a language to match? But, no; James Cameron inserted a brief shot of a monkey-like creature with partially-fused limbs, no operculi, and a single set of eyes to provide a half-way-there justification for the evolution of Na'vi people who are just like humans, actually.
Many animals produce sound by stridulation. No airflow required. Cicadas use a different mechanism to produce their extremely loud songs: they have structures called tymbals which are crossed by stiff ribs; flexing muscles attached to the timbals causes the ribs to pop, and the rest of the structure to vibrate. It's essentially the same mechanism that makes sound when you stretch or compress a bendy straw (or, as Wikipedia calls them, straws with "an adjustable-angle bellows segment"). This sound is amplified and adjusted by passage through resonant chambers in the insects' abdomens. Some animals use percussion on the ground to produce sounds for communication. Any of these mechanisms could be recruited by a highly intelligent species as a means of producing language, without demanding any deviation from an essentially-humanoid body plan.
There is, of course, one significant exception: birds have a much more flexible sound-production apparatus than mammals, and some of them are capable of reproducing human-like sounds, even though they do it by a completely different mechanism (but it does still involve expelling air from the lungs through the mouth and nose!) Lyrebirds in particular seem to have the physiological capacity to mimic just about anything... but they extent to which they choose to imitate unnatural or human sounds is limited. Parrots and corvids are known to specifically imitate human speech, but they do so with a distinct accent; their words are recognizable, but they do not sound like humans. And amongst themselves, they do not make use of those sounds. Conversely, intraspecific communication among birds tends to make use of much simpler sound patterns, many of which humans can imitate, about as well as birds can imitate us, by whistling. So, sure, some aliens may be able to replicate human speech--but they should have an accent, and if their sound production systems are sufficiently flexible to produce our sounds by different means, there is no reason they should choose to restrict themselves to human-usable sounds in their own languages. Similarly, humans may be able to reproduce some alien languages, but they will not sound like human languages--and when's the last time you heard a human actor in alien makeup whistling? (Despite the fact that this is a legitmate form of human communication as well!)
The most flexible vocal apparatus at all would be something that mimics the action of an electronic speaker: directly moving a membrane through muscular action to reproduce any arbitrary waveform. As just discussed, birds come pretty close to capturing this ability, but they aren't quite there. There are a few animals that produce noise whose waveform is directly controlled by muscular oscillation which controls a membrane, but they are very small: consider bees and mosquitoes, whose buzzing is the result of their rapid wing motions (or, in the case of bumblebees, muscular vibrations of the thorax). Hummingbirds are much bigger than those insects, and they can actually beat their wings fast enough to create audible buzzing sounds (hence, I assume, the name "humming"bird), but they are still prety small animals. And despite these examples of muscule-driven buzzing, it seems rather unlikely that a biological entity--or at least, one which works at all similarly to us--could have the muscular response speed and neurological control capabilities to replicate the complex waveforms of human speech through that kind of mechanism. But if they did (say, like the Tines from Vernor Vinge's A Fire Upon the Deep), just like parrots and crows, why would their native communication systems happen to use any sounds that were natural for humans?
Now, some people might argue with my assertion that "any of these mechanisms could be recruited... as a means of producing language". That doesn't really impinge on my more basic point that an alien language should not reasonably be expected to be compatible with the human vocal apparatus, but let's go ahead and back up the assertion anyway. Suppose a certain creature's sound-production apparatus isn't even flexible enough to reproduce the kinds of distinctions humans use in whistled speech, based on modulating pitch and amplitude (which cicadas certainly can). Suppose, in fact, that it can produce only four distinct sounds. That should be doable by anybody that can produce sound ata ll--heck, there are more than 4 ways of clapping your hands. With 2 consecutive sounds, you can produce 16 distinct words. If you allow 3, it goes up to 80 words. At a word length of 4 or less, you've got 336 possible words. So far, that doesn't sound like very much. But then, there are 1360 possible words of length 5 or less, and 5456 of length 6 or less. At a length of 7, you get 21,840 possible words--comparable to the average vocabulary of an adult English speaker. The average length of English words is a little less than 5 letters, and we frequently (9 letters) use words that are longer than 7 letters, so needing to go up to 7 to fit your entire adult vocabulary isn't too bad. And that's before we even consider the ability to us homophones to compress the number of distinct words needed! So: we might argue about exactly how many words are needed for a fully-functional language with equivalent expressive power to anything humans use, but through the power of combinatorics, even small numbers of basic phonetic segments can produce huge numbers of possible words--indisputably more than any number we might come up with as a minimum requirement. A language with only four sounds might be difficult for humans to use, as it would seem repetitive and difficult to segment... but we're talking about aliens here. If 4 sounds is all their bodies have to work with, their brains would simply specialize to efficiently process those specific types of speech sounds, just as our brains specialize for our speech sounds.
Now, to be clear, this is not intended to disparage any conlanger who's making a language for aliens and using human-compatible IPA sounds to do so. It's an established trope! And even if it's not ever used in a film or audio drama, it can be fun. There are plenty of awesome, beautiful examples of conlangs of this type, and there's no inherent problem with making more if that's what you want to do. Y'all do what you want. But we should not mistake adherence to the trope for real-world plausibility! And it would be great to see more Truly Alien Languages out there.
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