Is it possible to make flying agent which avoids obstacles over certain height but fly over low obstacles?
It could be possible to do something with the Nav system however if your working with flying entities then a path finding system is not ideal. Try looking into steering algorithms http://www.red3d.com/cwr/steer/ UnitySteer would be a start
You could create an invisible plane to generate your mesh on. Have your low obstacles within the step height/slope value of your Navigation system and the high obstacles over it(or put them on a different nav layer). The problem is your flying object will always fly on a plane and wont really look like its flying.
Have one more question regarding objects like mine. If I have several different scales of agents. For example one radius is 8 units and other just 2. If I bake with navagent radius 2 units the big one starts to clipping obstacles if I bake with 8 meters the small one starts to fly a way far from obstacles. Is there anything I can do?
Found a sort of answer inside a thread: http://forum.unity3d.com/threads/navmesh-usable-for-multiple-radius-custom-agents.321585/
There is no simple solution to this at the moment. This user found a way to do it but its not simple: http://forum.unity3d.com/threads/pr...th-a-workaround-solution.178628/#post-1221631