pegasi have a lighter skeletal structure than other ponies which is highly adapted for flight. muscles make up a much higher percentage of body mass (due to the strenuous nature of sustained flight), meaning that pegasi are stronger than their earth and unicorn counterparts. the fact that pegasi are more susceptible to airborne bacteria means they have evolved superior immune systems; furthermore, the genes of sick pegasi who were incapable of flight were killed off by natural selection (pegasi who couldn't fly were left behind by the herd), unlike unicorns who just magicked the illnesses away and kept the crappy genes.
in conclusion,
get dunked.
Lighter bones work in the opposite direction of the point you're trying to make. Them being lighter means they're likely more brittle and easier to break. So either you're wrong, or you're proving a point that makes pegasi inferior.
Your muscle argument is also flawed, in that flapping wings doesn't build muscle in any other part of the body. As such, ponies that traverse on ground are likely to have stronger leg muscles while pegasi that primarily get around through the air have stronger muscles needed for using their wings. This is also different on an individual pony basis based on genetics and different daily routines that may use different muscles, not to mention body building, which is something all pony races can do.
As for airborne bacteria, pegasi and other ponies breathe the same air. The altitude of said air is negligible. And considering there's a lot more on the ground that could get ponies sick OTHER than airborne bacteria, and if pegasi live in the clouds all day, if anything, there's less to build up their immune systems.
A pegasi that couldn't fly could live the life of an earth pony, no problem. So not being able to go with other pegasi shouldn't be an issue. Also, regular pegasi aren't ******** like Leaf, and if unicorns could cure them, they'd likely seek them out.
Unicorns natural selection likely occurs more from those less adapt at magic not being able to live as well as those better at magic, and not from illnesses.