I prefer Aeris and pronounce it "Ay-er-iss." It kinda sounds cool with that extra half-syllable. Plus, consider this entry in Notre Dame's online Latin-English dictionary:
"aer, aeris: air, atmosphere, ether, weather"
In FFVII, there seems to be a connection between the Planet and the wind (i.e. Breath of the Earth, Healing Wind). There's also other passing references if I remember correctly. So it makes sense that Aeris' name should be based on the Latin word for "atmosphere."
~MJE~