A post I saw suggesting random encounters on the ferry reminded me about how Setzer informs us that the "skies are a lot unfriendlier these days." foreshadowing Doomgaze.
Well, that's great, but wouldn't it make more sense if Doomgaze wasn't the only thing flying around up there that wanted to eat you?
I submit that there should be more random encounters in the air that the party needs to deal with outside of Doomgaze. There are already suitable backgrounds that wouldn't need to be modified, and plenty of flying creatures to use. It would also allow for an element of surprise when Doomgaze actually appears, since at this time everyone knows that the only air encounter is Doomgaze.
In addition to randoms, I also suggest that another boss encounter be added, one you can't just select to chase down. Perhaps one of the legendary dragons could be flying around menacingly? Perhaps a mechanical horror set loose by Kefka?
One final suggestion would be more complex, but what about a script event, perhaps after the party first fights Doomgaze or any other air battle, where the Falcon gets damaged and is forced to land on Triangle Island, where the party is forced to wait until repairs are completed. They explore the island, encounter the Zone Eater, and after recruiting Gogo the Falcon is repaired.