Typically, from what I know there are very few birds that fly more than a few thousand feet off the ground. So I'd extrapolate to that to flying critters.

I'd restrict the airspace around ANY airport as controlled airspace. Where small airports are similar to Class D airspace defined by the FAA. Any vehicle or creature in that air space needs to have two way communication to talk to both ATC and each other.

Cross-country travel over 200 knots outside airports would be done at an altitude above say 5000 feet. Below that there would need to be a speed limit, nav lights, and enhanced anti-collision lights to enter uncontrolled airspace less than 5000 feet.

Mix all that with common published approaches and departures, airways and ATC you could have a safe airspace I think.