A well balanced stamina mechanic would be a great way to implement flying. (Something along the lines of Valheim and Breath of the Wild's stamina mechanics)

With some tuning not only would it prevent complete flyovers, it could actually be really fun and add another option for progression. Like a basic mechanic where climbing altitude quickly consumes stamina, while gliding consumes it slowly. Add thermal drafts to strategic locations and let the player improve their flying stamina over time.

Now you can limit how much a player can fly and when, and create fun game moments with crash landings in hostile areas when you misjudge your stamina.