Hammond Robotics
With regeneration explained, the process of mind uploading makes much more sense. An injured pilot can upload their brain through a misappropriated neural link, and a dead pilot uses the backup created in the regeneration procedure. That also explains why there was no backing up in the Tf1 regeneration, as there were no simulacra. There is still the mystery of who created the simulacra, filled by Mr. Hammond (son of Dr. Hammond). In Tf1, it was stated by IMC grunts that he was working on a replacement for specters and that it involves, "synthetic biology". This rather fits the idea of a simulacrum. A robotic pilot that excels in combat far above that of a specter. It fits the theme of synthetic biology not in the sense of replicating organs or blood or muscles, but by replicating a human brain onto a digital format, and therefore allowing a human mind to run on any mobile hardware.
In the map Colony, the Militia grunts have a suspicion that it was "only a matter of time before Hammond started building a synthetic pilot". While this quote is useless on its own, it gives credibility to the other evidence of Mr. Hammond's work. There is also a quote on the Spectre Camo burn card by Hammond, about how he's not "throwing away their humanity", but rather "discarding their human frailty." It seems he is trying to reassure pilots about having their minds crammed into a robotic body. In this case an early spectre prototype rather than a purposefully designed body. These simulacra would be a massive advantage to the IMC's war effort during the war by creating infinitely respawnable pilots that need zero training as they already have combat experience.
However, by Tf2, it seems the simulacrum and the digital-copying technology have become more widely available to all factions, as we have seen new simulacrums that are created using minds that are not loyal to IMC. In fact, we see simulacrums that are free to work for any faction they choose, rather than being kept close to either side in the Frontier. I'm not entirely sure how this monumental advantage for the IMC was lost to the Militia, and there is still the question of who is creating the simulacra.
