No, there's no way they're going to use the Youswell story or the train-hostage thing. (I'd only include the train-hostage thing because in the absence of the Ice Alchemist episode, we lose the introductions of Mustang, Hawkeye, and Hughes, which, in the manga and first anime, occured in the train-hostage episode.) So I will have to use these episodes, slightly edited of course.
There's also May Chang's introduction in Youswell later in the manga that wasn't in either anime (since May wasn't in the first anime at all). I highly doubt they'll include this at any point, which is sad.
I'm holding out hope that future episodes will include more Ishbal flashbacks, so I can fill out that episode into a two-parter (I'm definitely moving Scar's Ishbal flashback into this episode, the way it was in the manga).