How can I counter a flying character?

Fireball with a cone of 30 ft would be translated into a spherical form causing an Aven origin character to crash

Then what do you do about the human Wizard who chose the small size, two origin feats, and Find Familiar? There are medium size familiars a small creature can mount. You can't ban that or enforce a level restriction without singling out the player. Consider all of the other racial options that are comparably powerful as a flying speed. Climbing, and extra movement speed is available for a Tabaxi, which can drag a grappled enemy up 30 feet (half of their 60ft movement from their trait) and drop them. A flying species is limited to 15 feet. They can keep their distance either by moving out of range or climbing a structure/wall in the environment. There are species with teleportation traits that get around issues even flying can't solve. A plasmoid can fit through a hole at least 1 inch in diameter.

Dragon

Nets and the catapult spells with a net is great against flying creatures. Thornwhip spell, hold person, web, hypnotic pattern, sleep etc are all great spells to have a flying creature fall. Ultimately, let them have fun flying about 

Quote from Delvesdeep2 >>

Nets and the catapult spells with a net is great against flying creatures. Thornwhip spell, hold person, web, hypnotic pattern, sleep etc are all great spells to have a flying creature fall. Ultimately, let them have fun flying about 

 Catapulting a net is not going to work (unless your DM says otherwise, of course). The catapult spell just does damage. Allowing it to effectively impose the restrained condition is big change to the spell.