The game is fairly open, so you can challenge the Gyms in different orders, though there are prerequisites for a couple.
If you press Down Arrow + X on the Title Screen, you'll enable Debug mode. It is recommended you make a backup of your save file first.
This also currently causes the game to crash during the special scenes with Typhosion at a bed. You can fix it by backing up the Data folder beforehand and replacing it with the clean copy afterward.
Talk to a woman in Clover if you have fucked Pokémon at least 5 times. The Scyther must be male.