The entire idea that Thargoids have an 'inherent vulnerability to guardian tech' is counter evolution.
I wish that CG hadn't worded it like that, it's very flippant and misleading.
The guardians developed technology which specifically targeted anything with Thargoid engineering in it. Saying they have an inherent weakness to a technology, without mentioning the deliberately targeted part, is like saying we have an inherent weakness to bullets without mentioning that they were deliberately designed to kill us with. It's not a fair representation when the mitigating factors are left out.
From the Guardians Codex;
4/28 : Thargoid Log – The War Machine
The data in this log details the methods used by the Guardians against the Thargoids. At first they deployed ground troops, but when this proved ineffective they started to use drones – autonomous machines that felt no fear, fatigue or uncertainty. These war machines became highly sophisticated in a relatively short amount of time, and were soon able to identify and target anything that utilised Thargoid engineering. Even more remarkably, Thargoid bio-mechanical technology was engineered to recognise anything of Guardian origin. That explains why, millions of years after the conflict, Thargoids devices still react aggressively to the presence of Guardian technology.
The way that CG worded it really muddied the waters there.
I do think however that it is wise, or what we humans would call wise, of the Thargoids to be wary of the only technology that has ever defeated them and which may have the potential to overtake them again if others learn how to use it or the Guardians return. That seems like an entirely sensible precaution.
If anything it would be the other way around. But I am not here to ruin it for anyone.
Second,
Evolution has demonstrated that symbiosis is the way. Just look at a human body. As much as 75% of your cells do not contain human DNA.
The only real answer is that perhaps, the Thargoids are from another place/region of space that requires a certain set of traits that are different from what is necessary in the milky way. -- Of course this would mean threats GREATER than the guardians require them to keep these traits (that allow for the inherent vulnerability)
But that is just my realist brain talking. I love this game. I roll with it.
Although Thargoids are carbon based their chemistry is ammonia rather than water based so I would be wary of one to one comparisons with human evolution. Biological and Technological evolution are also not the same thing. Saying they could simply out evolve guardian technology as if it was a straightforward biological process is again like saying we can simply out evolve bullets. This is a technological problem not a biological one.
In that respect the Thargoids may be more integrated than humans since they are literally described as bio mechanical. Which would logically make their "combined evolution" faster in some ways and slower in others, with both biology and technology having to evolve or be engineered in their own specific ways in order to compliment each other.
And of course as soon as you introduce technology to counter what biological evolution cannot, you are no longer evolving naturally but forcing the issue and attempting to take charge of it, or as much of it as possible. So what might happen in nature ceases to apply in any case. We stopped evolving fully and directly to the natural environment when we made fire, tools and shelter.
As for how Thargoids adapt that appears to be selective. Assuming they can out evolve anything with the same ease no matter what is actually involved, as unlikely as that is, it may be a case of priorities.
It seems that large threats like Salvation's superweapon they adapt to very fast, within three or four uses of it they had immunity. Years ago a Galnet article noted that they were adapting to human weapons so they were less effective (although that was in order to introduce us to guardian weapons), yet we have been killing them with those guardian weapons ever since and they have not adapted at all. Gauss are as effective today as when they were introduced years ago.
So what they adapt to appears to be based on some other criteria than "oh it's a threat we must adapt immediately".
Perhaps it is about how dangerous they consider a threat. Better drone killing weapons like guardian gauss are therefore unimportant because individual drones are unimportant, compared to weapons capable of mass slaughter like the Proteus Wave.
But even then there may be limits to what they can counter. Again, the Guardian Codex tells us that the technological development of the Guardians was rapid once begun. If the Guardian AIs are still alive they have had a million years to evolve their technology in secret, and what we've found so far at their sites and ruins could be the tip of the iceberg. Salvation the supermuppet's attempt to upload his ego into a Guardian box confirms that there are still things we don't know about their technology, and possibly new items to discover.
If it comes to that we don't fully understand what Guardian stuff we have already found. From the Guardian Codex we know that Relics are part power source, part computer and part key and were apparently programmed to run specific tasks. We know all that, and not one thing about how to program them ourselves.
So in that sense there is every reason to think that the Thargoids are right to be wary of technology with the capability to develop faster than their own, and which targets them in the process.
Their minds have been tampered with maybe.
Again IIRC they've been described as traumatised by their experience, which is perfectly natural, but no evidence that they have been brainwashed or otherwise influenced. But then they could be sleeper agents so it hasn't happened yet and the trigger will be telepathic when the time's right. We'll know soon enough.
I don't have much to contribute aside that while I would also enjoy a good twist, I believe the narrative might stick to some tropes as this is what most people enjoy (why we have so many action movies about the same stuff while truly original movies are harder to find).
From my point of view, I don't see the Thargoids as aggressors but then the game experience, especially for fighters, would be quite dull.
Here's to your cool theories and hopefully something cool nobody saw coming
With so little to go on that wouldn't be difficult but yes, that would be fun.