Aeris being representative of the earth, Nanaki being of the earth, and Hojo being thoroughly representative of the alien crisis from the sky. You probably haven't read much of my FFVII stuff, I have this thing about Jenova being a genetic invasion - all it wants to do is turn all genetic codes into replicas of itself. So given freedom, the whole planet would be Jenova and nothing else, then once that's done it blows up the planet to shoot more of its genes out into the universe to begin colonising again. Aeris thoroughly embraces the idea of Nanaki as a lover, however awkward the circumstance, because all their lovemaking and/or furry children would reinforce the idea of diversity that is Gaia.
Aeris is very good at seeing to the core of things, and saying exactly what people need to hear. Cloud's instant adoption as a bodyguard, for example. Nanaki needs to be saved, Cloud needed to be needed, so on. She's blissfully frank, compared to some muses...