Just no. Give us an ingame money sink or maybe even a cool down or something. But make making fly another "pay to have the game a lot easier than it is for non members but not p2w" is a really bad idea.
Do you think people are going to want to have to travel for possibly hours worth of time just to make a simple trade, battle or meet up with team members? The answer is no. Hindering fly to an essentially member feature would be a bad choice in respect to your whole player base in terms of how you want the game to be played. Essentially solo, with some player interaction, or a pokemon MMO, where people need to be able to meet up and trade, battle, or catch pokemon. You can't treat fly like you would in most MMOs because in pokemon the pokemon from previous areas can still be needed, and need to meet up with players who arent as far as you, without it taking an extreme amount of time
I agree with Jate, this game is showing actual potential- But it's when those types of features that are added that scare off people who just want to play pokemon with friends. Fly is pretty much the one of the mechanics players rely on most- both starting the game and ending it. Putting even the smallest of fees or adding a donation-based cooldown is adding up to an expensive travel route for trades by itself. And I'm sure I speak for some when I say that adding this would only cause frustration other than an actual obstacle of sorts.