I really like your patient ecological twist on the aliens, that fits well with their way of acting in the games:
Yeah, I saw there was a plethora of reasons that they needed to be a relaxed, slow-paced people. Us not standing a chance of fighting them notwithstanding, were our planet invaded by an aggressive race like humans, it would be blindingly obvious they're here.
Assuming what we read there is true (and genetic lineage should be easy to assess in the times of TftD), Gillmen were active amphibious reptilian beings during the time of the dinosaurs (a reference to the fabled "intelligent dinosaur", I guess) that were mostly destroyed at the same time as them, when T'leth crashed on Earth. At that time, they entered a symbiotic relationship with the aquatoids, presumably helping the survivors with local knowledge and manpower, while the aliens provided technological support that enabled the species to survive the cataclysm (maybe prompted by their guilt at destroying the current order of the planet, going by your ecological take on aquatoids).
That's a neat take on it. Maybe the aliens altered the Gill Men and later Mutons and Humans to look like them. Maybe they coerced our development slowly, biasing us toward a specific form. Tasoths could be an earlier iteration of what later became the Gill Men.
Another comment I had is that I'm not sure of the usefulness of introducing terranoids. It would make a lot more sense for the aquatoids to be like they are if there was little land on their original planet. T'leth would have been sent early in their history, before the apparition of terranoids and sectoids), as the aquatoids' first foray in space travel. Maybe they realized that sending water laden crafts in space was not a great idea
The longer they spend on land, the less it makes sense that they would send aquatoids to settle other planets, and especially that the aquatoids of T'leth didn't have access to the sectoid strand to help them fight the ground based humans, or take control of the world in the millions of years that they had.
Their planet is mostly ocean, like ours. At first, only a small fraction was habitable, slivers along the shoreline. But as their technology grew, they inched their way deeper and deeper, and eventually they could live on the bottom of the ocean. By the time they were capable of going that far, they were also able to control their population size. There was no need to go on land, so they didn't do it. They studied the stars I'm sure, as they were a watchful people, but they wouldn't have thought there were other planets out there.
When they decided they had to expand beyond the ocean, the land was the obvious choice. At this point, much of their technology was far superior to ours, having been in development for over a million years past computers. They still didn't know other planets existed, because it wasn't important to them. They built terratoids because it brought them resource efficiency for over a million years. It was their first major alteration to their own genome. Sectoids came much later as an advanced form, when they had a lot of experience both with the rigors of space travel and with altering their genome, and probably they sampled genes from life on rougher worlds, microbes surviving on worlds that lost their atmosphere, perhaps.
They probably sent Aquatoids into space for any of a few reasons:
1.) Aquatoids were around 75-80% of their population
2.) Terratoids were weak, energy-inefficient compared to Aquatoids
3.) They needed to bring water along for long distance travel anyway, to protect against cosmic rays.
But maybe I'm wrong and they would have sent Terratoids. It's not important really, I think I've decided pretty firmly at this point that the Aquatoids aren't the founders.
Finally, I think making The Great Dreamer the "founding species" would be interesting. The cydonian brain could be an evolution, after millions of years emphasizing psychic control at the detriment of everything else. The Great Dreamer is a formidable being that could stand against humanity should it be awakened, but it needs implants to control its minions, whereas the brain can't do anything, but it can control aliens through sheer psychic might.
That's a cool idea! Maybe it was a member of a race with lots of experience altering genetics. They had imbued themselves with the greatest traits they had come across or even invented, such as psionics. This one went rogue perhaps, and sought its fortune in a new sector of the galaxy. It's a bored megalomaniac maybe, trying to play God, and creating servants in its own image--although since its direct appearance is variable, it makes us look the way it envisions an ideal version of itself.
One last thought:
I had this idea a while back that they colonized Mars first, when it was lush--they considered Mars more habitable due to its lower gravity. They made a small Earth expedition which relied on supplies from Mars. The Martian climate destabilized and the Mars colony fell into minimum operational status and was unable to support the Earth outpost, so the Earth outpost went to sleep. They lived so slowly that they failed to react well enough to the changing climate. Fast forward to now, and the Mars colony is making trips to Earth to gather food and genetic material, as they continue to perfect their Mars climate resistance while also trying to beef up their gravity tolerance.
They wake up the Earth outpost as a last effort to survive. It goes into overdrive mode, depleting most of its stored resources in 40 years, preparing for an invasion.
Would be neat if we had all the tech from the first game in TFTD, and we needed it because what the aliens bring to bear against us after preparation is so much more fearsome...