I agree the math comes out that Fire II in the middle makes for more theoretical DPS but in real situations, I don't use Fire II at all as back to back Flares with the mana tick glitch fit very comfortably between Transposes. This is the AoE rotation I always use once in AF3:

Flare==>Transpose==>(wait 2s from first mana tick)==>Flare

That's it. The only time I use a Fire II or something in between is when I'm going to Swiftcast the second Flare thus leaving me with a couple seconds to spare before Transpose is up.

Also, in the spirit of April Fool's day and Yoshi-p avatars, I leave you with the following:

"Hai. Haihaihai. Haihai. Haihaihai. Hai. Haihaihaihaihaihai. Hai. Haihai. LOOK FORWARD TO IT"