So, a thought suddenly came to me. How is Ame going to implement the HM for Fly? It isn't exactly a necessary HM. But, we're going to have most of the HMs by the end of the game, if not all, right? RIGHT?
Anyways, I've theorized on a way that Fly might actually be necessary for the game! So, in the current release (SPOILER ALERT), you are still trapped in the Agate Circus area, and there are four definite gyms left in around there: Ciel's, Saphira's, Titania's, and Amaria's. And, as most know, Team Meteor has surrounded Calcenon City, and they're controlling Labradorra. Now, perhaps during an Episode, you must backtrack to Reborn City. Maybe you must challenge Fairy type leader Adrienn of Coral Ward? Or perhaps the PULSE is over there. Who knows.
But of course, Agate City is still asleep, preventing you from going that way, which is the only path. Sooo... Maybe you'll be forced to get the HM02, Fly, and the badge to use it (I suspect Ciel's) to get out of that area and continue story progression!
Just a little thought I had, pure speculation. But Ame might just be sadistic again and never give us Fly, so we have to keep walking back and forth from area to area. (PLEASE DON'T DO THIS AME)