Yeah, I've done a lot of thinking on the Fulbright thing, and more or less came to the same conclusion that you did about the Phantom killing him assuming his identity, since it actually makes the most sense, and is also comforting in a way. While not specifically stated, I think it's the most logical conclusion based on the given data.
I don't recall a lot of the specifics from the older games (memory issues, yay~), though I do plan on replaying all of the other games now that I've finished AA:5. I do kind of wonder, though, how much my memories of taking down some of the big baddies (speaking of which, you're right, Alba was excellent, even if memories of him did make me somewhat wary of Yuri at first, ahahahahaha) was either A) nostalgia, or 2) the difference in difficulty. I felt like this game was really hand-holdy at points (basically flat out telling you that you need to present X thing in a "thought bubble", argh), which may also have contributed to making it less satisfying. Doesn't really matter, though; I'm sure I'll have just as much fun taking them all down again.