I'm stuck on the flying thing. Here's another suggestion for connecting the dots...
Clark's heretofore disinterest in trying to fly could be explained as a result of the physical pain he experienced as a kid in Pete's tree house. Kryptonite made him sick when he was in a high place, and now through subconscious association, that pain has manifested itself into his adult acrophobia.
The writers are always looking for ways to make Clark relatably "human." It's what makes SV special, and separates this version of the mythos from so many others. Here's another opportunity to "ground" the character with a psychological flaw that many people have, but are perfectly capable of overcoming. What better way to show how irrational this particular phobia is than saddling Superman with a fear of flying? That's writing genius!