TenForward: Where Every Vulcan Knows Your Name

I know that they actually have a bit on trek canon that most life in the galaxy was preceded by a progenitor race, which explains why all the aliens look like humans with junk glued to their heads.

But my head canon has always been that in Star Trek, there are actually innumerable alien species of all sorts of body plans and configurations. Hell, we meet plenty of non-humanoid aliens in the series. (Any number of floating energy creatures, plus some number of non-bipedal creatures, aquatics, etc.) What we see on screen is simply not a representative sample of the galaxy's denizens.

My head canon is that the Federation deals primarily with humanoid species. They're not racist; they'll happily let in non-humanoids and treat them with full equality and respect. But the truth is that when working with aliens, the more alien they are, the more difficult it is to find common ground. And further, there's just less reason to form complex diplomatic relationships.

Imagine a species of nonhuman aliens that can only exist in the crushing depths of the atmospheres of gas giants. They communicate primarily by passing radio waves between each other, they are completely blind and deaf, and they have a communication structure that makes the Darmok problem look simple.

It would be very difficult to see such a species joining the Federation. First, they can't communicate effectively. There aren't even auditory sounds for the universal translator to translate. Second, there's little reason to communicate. This is a species that has zero interest in the Earthlike terrestrial worlds inhabited by most Federation species. This species and the Humans and Vulcans aren't competing for the same real estate and resources. There's no need to carefully negotiate territories and access. Such a species could operate their own independent federation right on top of Federation territory. Two parallel interstellar empires could be operating out of the same systems and yet barely need to interact with each other.

This is my head canon for why most aliens in Start Trek are humanoid. The truly alien aliens? There's just not much to negotiate over. There's little need for diplomacy. If your minds are so alien that your cultures mean nothing to each other? If your biology is so different that you're not even competing for the same resources? If you have trouble telling if the alien entity you're interacting with is even sentient? Then no, there's just very little reason for such a species to join the Federation.

We do sometimes see non-humanoids in Star Trek, but these are likely the outliers. The most gregarious of non-humanoid species. They get involved with the Federation simply because they want to. They're naturally curious and want to understand these weird humanoid aliens, even if there's little practical reason to do so.