Portal headcanons in no particular order, subject to growth:
The cores, nanobots, and other fully or semi-sentient AIs were largely disregarded by the staff of Aperture, and had developed their own private little social circle right under the humans’ noses long before neurotoxin was released in the Enrichment Center and Aperture fell into their care.
Translating Caroline into code gave the scientists the secret to creating true artificial intelligence, and they never stopped to consider what that meant. Behold, cores.
Caroline had always been the brains behind Aperture Science.
Virgil, the Maintenance Sphere, is good at hacking because that’s the only way you fix anything in Aperture. He doesn’t have hands, you know, and only GLaDOS would have the Mainframe’s admin access over Aperture machinery. Gotta repair the facility somehow.
There are many cores, but the Enrichment Center is so huge and labyrinthian it’s hard to track them down.
Cores might give themselves human names to create a semblance of an identity, which, pre-Bring Your Daughter to Work Day, would’ve dissuaded humans from looking down on them as simple pieces of tech. Wheatley also used his name to cover up his true purpose.
Wheatley’s cowardice is both a result of and a coping mechanism for his own programming. If you’re constantly making mistakes in a place like Aperture, you’d better be good at not dying.
Virgil is the only personality sphere so far without a designated personality, only a function (maintenance), which may be why he called himself “simple” during his introduction.
Wheatley can be clever and genre-savvy on occasion because he has experience learning from mistakes, and planning accordingly.
Atlas and P-body are basically really smart children. They’re both way younger than any other robot in Aperture.