My version of Smallville would have had him flying as a teenager, like once he hit puberty, flight should have been natural to him. However, while he could fly in my Smallville, he might not have it fully mastered until his training with Jor-El, so comedy would ensue when he starts flying too fast and can't stop in time, or to slow and falls to the ground, or gets kinda squeamish at high altitude and freaks out, etc.....
My Smallville would have 4 years of HS, then transistion to College, he could go to learn to become a Journalist, what a novel idea. Then he'd decide to go off to training and that would take a couple years at least (this would happen over the summer break though, we'd pick up 2 years later for the next season), and we'd have like half a season of him in the Fortress mastering his powers and figuring out how to go back into the real-world with a dual identity, during that time we could see him making "blur" rescues (but in the cape), kinda testing out how the world might react to a superhero out there, without his face being seen yet, then later on there would be the big reveal as superman on some grand save, and then we'd have a whole season of the New New Adventures of Lois and Clark for at least a year (ok maybe i'm dreaming with the last one)