skygiants

Yeah, that's pretty much it. The Company series is what happens when a fascinating idea is thoroughly treated by a capable writer who doesn't know when to stop. Up through book 3, maybe 4, it gives Mendoza and Joseph unconventional immortality and plays with it all, using The Company as the evil antagonist in the background. Many of the short stories are fun snapshots, especially of the gross way The Company works.

Then it turns into The Fate of the Human Race (and Neanderthals), which seems to require inventing a lot of dubious genetics and a whole sub-species of etiolated little people from... underground... Oh. Actually, this fits very well into your picture of Mendoza-as-Mary and the tripartite Nicholas-Edward-Alec as immortals who eventually displace the Jupiter/Zeus Company. Non-immortal humans absorb the folkish-fairy elements, which overall makes them less able to survive without the Company. There's an inexplicable side plot about The company manipulating Alec into blowing up -- I think it was Mars, actually, but whatever -- which doesn't stop him from enacting his One Third of New God role. This is all a take on Mendoza's Catholic Christian early life, as if the whole series were meant as her dream of what immortality makes her into.