Other than that bug I reported I do really like this game. The beginning felt a little weird difficulty wise but once I got past Canaveral City things balanced out. I do suggest opening up the Department Store in Canaveral City and just limiting it to the first floor until later in the story...
I downloaded and played your game a while ago but have recently restarted so I can take in all the new graphics. Wanna say that this is so far one of my favorite fan games and I can't wait to see the finished result.
I saved but I did eventually figure out a way to get off the pokemon. Had to go back into the mud and then try and get out of the mud prompting it to ask me to ride the pokemon then I flew out and went back to the mud and repeated and was finally able to get off it.
Need to report a bug. If you fly while riding a pokemon you permanently get stuck riding the pokemon. Movement speed is insanely slow so it's a bit of an annoyance, not game breaking just annoying. I tried going into caves, gyms, using teleport pads and even surfing and nothing resets it.