Listen to the Rain

The problem is that, without knowing the infrastructure of how a pattern develops or what it's for, the collection of species traits can wind up random.

As you say, if there's a physiological reason for it it works, but it often doesn't go that far. If elves appeared from the shed tears of the gods (or whatever), then maybe they get +1 with bows because that's what the gods want, but without divine intervention it makes more sense to develop physiological traits and extrapolate from there. If elves are good with bows because of their superior senses and hand-eye coordination, are they also good at targeting spells? What about delicate artisanship? Why is it just bows?

I mean, the Doylist reason is because Legolas used a bow. If Legolas had thrown spears elves would get +1 to that.

Alternatively, you can give them a master key, the Gift of Tongues; or a base language everything can understand, like Allspeak or Prime

I have seen some settings that do that, and it does make sense! It's just a personal preference for settings that don't have activist gods that makes me want another basis for a language system.

I can top that. Coyote & Crow is a game about a noncolonized Native American culture.

I remember reading your posts about it (though I didn't comment since I haven't read the book). There's certainly games I would be a little leery of playing with non-Jews--Dream Apart, for example, or anything taking place in the Dark Kingdom of Wire in Wraith: the Oblivion, but if the game is such that you would need to ban non-Jews from even playing it part of it, hmm. The solution is to find better players who will be able to properly engage with the material.

It's real, though. North America had a widespread trade language that touched all four coasts, Hand Talk or Plains Indian Sign.

You're right that there are various real-world examples of this kind of thing, like Hebrew among us and Latin among Christians for inter-cultural trade during the medieval period, or Chinese characters in East Asia (since they encode meaning, they can be adapted to other languages), but historically they're usually not a language of daily use--educated Jews knew Hebrew but they didn't speak it to each other, they wrote letters in it to people who didn't speak their local language--or they're a language imposed by some kind of empire on the populace. The fact that Common is humans' native language in D&D-land implies things about the setting that no setting designer ever seems to follow up on.

PDQ from Atomic Sock Monkey has been riffed across different settings, with very interesting results.

I've heard of it before, but to me (speaking personally) the system is too simple for me to really enjoy engaging with it. For some people that's a benefit, but I like mechanical complexity in my games and don't mind different resolution systems for different types of actions.

I had the same problem with the game Ehdrigohr, inspired by Lakota stories (I remember the author saying he took the game to a Lakota elder he knew expecting to get asked "What the hell is this?" but the elder loved the way he took inspiration without just trying to make a direct copy as an RPG) but really didn't like the way the system made every action boil down to "Attack, Defend, Overcome, Create an Advantage" which were mostly just +2 on a die roll. It was boring to play even if the setting was excellent.