I suppose that with Broken Steel, the gap widens as the Enclave guys get Hellfire Armour. 50 DR, best I have ever found.
Unfortunately. In-game, APA Mk II isn't much better than standard T-45d power armor, which is archaic and inferior in-lore. The reason the APA is about the same though, is likely because it can be found anywhere the Enclave is, which is alot of places. They'd have to almost make the armor non-playable if they wanted to give it its true lore stats.
The Brotherhood in-lore, is miles behind the Enclave in terms of tech.
There are more hints leading to Autumn who was with your father. I believe the president mentions something about him not being the same, after the radiation. Some other small hints I can't quite remember.
No, there were never "two" Autumns. Eden mentions that the Colonel and him hadn't been seeing "eye to eye" lately.
He survived the purifier incident, in which James killed himself.