My big concern around the hypothesis that the Thargoids are the Guardian AIs/Exiles/Hybrids is that the Guardians were highly advanced in biological warfare yet we, despite being less advanced, beat the Thargoids previously with the mycoid virus.
The mycoid was only myth and legend until recently but is now confirmed.
Also, the first Guardian civil war was between the tech merged Guardians and the anti-tech faction. That resulted in the exile of the Tech merged faction. The second civil war was over the AIs seeking existence as independent beings. It was between those that supported the AIs and the anti-tech/religious faction. No reason for the AIs to hate all Guardians when plenty of them fought and died for their right to exist.
There's been over 1,000 years of hyperspace travel. The Guardian bubble having been reached in that time is pretty reasonable. That's not taking into account warps and Galactic hyperdrives.
Not sure why humans would be Guardian descendants. I don't think FD would ignore the evolutionary history of humans on Earth which goes way way further back than the time of the Guardians. We share the basic skeletal structure of animals from 100s of millions of years ago on Earth, but we don't share the same structure as Guardians. Convergent evolution covers the similarities between humans and Guardians much better.
Also, indications are that it may have been us that attacked the Thargoids rather than the other way round.
Your first point: I don't think it's that the entirety of a mature and civilisation-spanning AI left and set up shop cranking out upgrades like the Matrix. I imagine the war was brutal, we know it ended the Guardian civilisation entirely, so it must have been epic. I imagine that a few surviving AI units escaped and slowly altered themselves over time, maybe they made lots of mistakes and were working with limited resources. It could even have been the equivalent of a few machines lying in a wrecked ship in a crater on some crappy ammonia based world after crashing there. Maybe it took them a million years to figure out how to walk, we don't really know how an AI (especially an Alien one, damaged by war) might evolve.
It may not have been the Guardian AI that evolved into the Thargoids, but there still
must be some significant link in the past between Thargoids and the Guardians that goes so far as to make the Thargoids react very violently to their technology in a way they just never have to us. If it was something like "we used Guardian stuff in the past", then why don't the Thargoids react as violently to us? As far as we know the Relics are inert things, maybe they are ancient weapons batteries (them rising up from the ground might suggest that), but that implies the Thargoids recognise that tech for what it is, recognise
it, not us using them, and not us as the beings that wield them, but the technology itself.
My theory, that there's a racial link between Thargoids and Guardians, makes sense of the almost instinctual reaction they show. It's like the reaction a Cat has to anything vaguely snake-shaped, it's hard-coded in ancient DNA because the two were ancient enemies. And, we only know of one enemy the Guardians had - the AI/Linked Guardians.
Your second point about the Guardian link with Humanity: Since DB and the team are scientifically oriented (while not strictly adhering to scientific fact) I don't believe they would "accidentally" create a species of aliens that look almost exactly like humans breathing almost exactly human air that
aren't related to us. Statistically that's incredibly unlikely to occur based on everything we know about evolution. Convergent Evolution accounts for small structures like eyes or certain organ features, but even then they evolved from the
same basic ancestor on the same planet so it makes sense that ultimately evolution would sometimes come up with very similar things given the same deck of cards to shuffle, but why would evolution create bipedal, bilaterally symmetrical animals on a
totally different planet unless they were related somehow? There's no reason that the ancestors of Guardians were 5 lobed organisms, they might have had six, or twenty, or three. Any minor variation back at the dawn of time would create wildly different end products, and sure they might have eyes similar to us, or maybe they have calcium-based bones because that's a handy thing to use, but it's far, far, far more likely that they'd be literally
anything else. We know on Earth that evolution has come up with millions of different answers to the same basic needs (food, protection, mating, etc.). Some species have wings, some are small, some big, some have tiny brains, some big, some are covered in armour, some fur, some scales, some warn blooded, some cold, some are mushrooms... Convergent Evolution wouldn't create a species that looks almost exactly like humans, or rather, it's so statistic incredibly unlikely that it's certainly not going to happen in almost the exact same region of space! If there are other Human-forms out there it's more likely they are on the other side of the universe or something.
What you're suggesting is that because a pack of playing cards dropped by Bob the Gambler landed with more Clubs facing up than any other suit, if you drop 52 bananas from an albatross they'd land with more Clubs facing up too. It just doesn't make sense.
There's so many factors that guide biology over an evolutionary process. The chances of two bipedal bilaterally organised oxygen-nitrogen breathing creatures naturally evolving in total isolation in almost exactly the same area of the galaxy is literally astronomical - Especially since the entire rest of the Galaxy (as far as we know) is totally uninhabited by sentient space-faring races, yet is equally littered with Earth-like worlds.
There's many ways the Guardians could be our progenitors that could intersect with what we know of our own evolutionary history. There's got to be literally thousands of Sci-Fi books that deal with similar topics, some better than others! Sure, none of them happened in real life, but it's stunningly unlikely we'll encounter sentient insectiod aliens that talk in morse code too, so there's some narrative lattitude given to Elite Dangerous game genetics
That brings me to point 3: There MUST be a connection between the Guardians, Thargoids and Humans that goes back to our 'birth' as a species. It's simply that we can understand each other. Ram Tah fairly easily translated the Guardian data without any frame of reference. We can understand the basic principles of the layout of the ruins, they seem familiar (the layout is not dissimilar from things we build), the scale of the obelisks is basically human-engineering-sized, the overall scale of the Ruins is human-like. Etc. etc. Same with the Thargoid stuff, it's all things we can understand. They use visible light to communicate in very similar ways to us (red is bad, etc.) They make sounds we can hear and interpret with our ears. The scale of the ground facilities indicate they're much bigger than us but not impossibly so. They use morse code, which means they must have learned it from us I guess? They behave in ways we can understand (for the most part) They use doors with keys, they use logic in similar ways to us, they view things similarly to us (the hologram in the central base chamber, etc.
The very fact that both the Aliens we encountered are: a) Understandable, b) share structural, societal and cultural similarities to us, c) occupy the same area of an otherwise empty Galaxy means there must be a connection.
