It's hard to keep up with the SF lore. There used to be a plot guide by TiamatRoar that really helped, but it's changed hands over the years and recently, the newer guy in charge was shown to be inaccurate and twisting facts when it came to the SF4 era -- he kept claiming that the Japanese versions told a different story, despite all versions of Guile's opening saying Charlie Nash it, "wasn't really his full name", this isn't canon, that isn't canon etc.
The most notable example was that he said the Japanese versions of SF 4 showed that Gen and Gouken were dead, but these characters that are playable were puppets raised and/ or created by S.I.N.. Gen in particular was supposed to "have remembered dying" and Gouken showed hints in his dialog that he was a clone who thought himself to be the real deal. Finally a few people on SRK kept clashing over stuff like this in the "Warrior's Fate thread" and eventually asked a guy who lives in Japan ( I can't remember his name, but he's a respected member of the community and is fluent in Japanese) he immediately debunked a lot. After this, the newer guy, threw a tantrum, killed all online versions of the plot guide (even though the old and original versions were made by TiamatRoar) and disappeared for a while. He recently popped up again and started updating the guide again. So because of this, people are unsure of what to trust in the guide, which is a shame because there's a lot of good info in there, but there's some false info being presented as fact when it's just loosely put together theories.
My advice, is to take a look at the whole thing if SF lore interests you, but be VERY VERY wary of the entries on SF 4 and beyond. Things prior to that were fine since they separated theory from fan speculation presented as fact.
About Gill, all we really know is he and Urien were raised from childhood into the Secret Society cult to be the next leader -- the worthy one was the latest reincarnation of their great and late leader. Because of this, Charlie and the blond kid the Boxer stole aren't candidates, though we don't know if SF3 is going to face major retcons, so anything is possible. It would be a crazy and interesting twist if Charlie, so disgusted and horrified by the corruption of the world took it upon himself to become the dark hero the world needed, went big boss and became Gill, though pulling off that would need a complex story and if handled wrong could torpedo everything about his character.