Yeah, it's basically an AU. Actually, I guess it would be more accurate to say that the original anime was the AU, since the new one follows the manga, but whatever. *g* (I love how fandom gives us such a useful metaphor for this kind of multiple-canon situation!)

And yeah, I agree with you about the end of the anime definitely leaning towards Roy/Riza ... but still not in a way that couldn't be read gennishly, I think, or at least as being one-sided on her part -- you could kind of fill in the blanks. (It made me very happy, but then, I have certain shippish tendencies for those two. *g*) No idea how the manga and new anime will work out, though.