For it to be useful, it needs a beneficial nature (Timid is best, followed by Modest) and properly distributed EVs (252 Special Atk, 252 Speed). You need the Move Reminder in your Secret Base and a few Heart Scales to give M. Flygon its best moves as well, namely Drakon Voice and Ancient Roar. It gets Bug Buzz at level 50 and Boomburst at 54. Other options are Earth Power, which it gets at Lv 26 (you’ll need to have learnt it as a Vibrava IIRC, since Flygon evolves at LV 45) and Flamethrower/Fire Blast, which are both found later in the game. If it still isn’t working for you, you might need to rebreed it for higher IVs (basically inherent numbers that dictate a Pokemon’s potential). Higher IVs mean a stronger Pokemon. There are guides for pretty much anything you need, be it EVs, IVs, or breeding, depending on your familiarity with the terms.
basically what mad said. tho thats for competitive. if you want a good m.flydon for the story you dont need to worry about natures, evs, or ivs. just give it sound based moves like drakon voice and bug buzz(stab) boomburst which is stupid strong and boomyou got a good m.flygon. btw it is NOT a physical attacker, i have this feeling you flygon is physical hence why its bad