Let's see.... a few interesting ones here I would like to take a crack at. I don't read the comics, so I can only base my opinions on the show.
The Great War.
I have not fully developed all the details of this in my head, but I think it was a false flag operation by Julian. With a military of entirely robots, it would be easy for him to start a false war. SatAM never gives any details about Sally's mom, so here is a very rudimentary thought on it. Julian found and began experimenting with the Roboticizer. Somehow, unfortunately, the Queen became aware of his autrocities, and he roboticized her. He then hid her, blamed her disappearance on some faction, and started the War. This would allow him to continue his experiments and build up the army until he was ready.
Roboticization
I agree that it is done by nanomachines. But instead of fully converting flesh to metal, they work with the biology a la cyborg. Power rings have the ability to distrupt function for a fime, returning freedom of will. The failed deroboticizer in Knothole could deactivate the nanites for a time, but they revert to their original programing after a time. I also suspect that there is a massive transmitter that Robotnik uses to maintain the stability of the nanite programming, which makes it hard to deroboticize anyone once the nanites are implanted.
French Antoine
I don't believe the rest of the Freedom Fighters are actually speaking English, especially since the writing as seen on the show is *rarely* English. As a watcher of anime, I consider any "English" seen or heard in SatAM is merely dubbing and localizing. As such Antoine is not really speaking French, but the closest human equivalent is French. This would be similar to how Osakans in anime are sometimes given a Southern-esque way of speaking when dubbed in English, since Osakans are seen a the rednecks of Japan.
I love my God, my wife, my 5 kids, and I like my guns, my beer, my whiskey, and my pickup.
I dislike politicians, policemen, diet foods, no-smoking signs, and mowing the lawn.
I like Sonic games from the Genesis days, tolerate the Sonic Adventure series, can stomach Sonic Heroes, and can't stand the rest.
And there is only one true story of Sonic, SatAM.