TwoTHREE major things.
"Maeda: A system like Phoenix Mode which lets fallen characters revive the very next turn I thought to be system ill-fitting of FE. However, it was deemed necessary for players who may think, “This is very interesting, but seems much too difficult for me. But with this mode, maybe even I can play it?” With these players in mind, this mode was born."
So even some of the developers agree that Phoenix mode doesn't fit with the themes of death in FE. At least this will end some forum debates.
Do characters who become allies also appear as enemies on the other path?
–Maeda: Yes. They appear as quite formidable enemies even. While we had done the idea of fighting a friend turned foe in the series before, it was not implemented on a grand scale. As this game was developed on a grand scale with branching storylines, we believe the system was implemented quite smoothly this time.
So we do kill the Hoshidan Scum our stalwart allies if we play both routes. Glorious! Waifu killing galore! WHEEEE!
Finally, it has been confirmed that Aqua is a Nohrian Princess kidnapped by the Hoshidans. In otherwards, either the Hoshidans are petty kidnappers who did the exact same thing Nohr did to Kamui, or the Hoshidans kidnapped Kamui first and Nohr retaliated. Well, it could have been a mutual trade but who knows? All that matters is that things aren't so black and white anymore.