I have a handful of ideas all revolving around the Smallville series. Some use the setting as a loose template, others draw off specific events. In either case, the show would be more of a starting place than anything else.
1. A Fallen World (Clark/Lois)
Several years in the future, in a time where Clark has accepted his destiny as Superman, disaster strikes. Shadowy forces attack the earth, and though Superman tries to stop them, he ultimately falls.
Unwilling to accept defeat, his wife, Lois Lane, travels to the fortress and uses it to travel back to a time when she first met Clark. She finds herself inhabiting her body from several years ago, with all her memories and experiences from the future. It is her hope to convince him of the coming threat, and to use her knowledge of his full potential to train him to become someone who can save the world and succeed where he originally failed.
(This is a vague little outline, but you get the idea. The idea here is to pair Clark with a slightly older Lois, at least in mind. She would be more experienced than him in the ways of the real world, as well as her knowledge of their relationship. Clark wouldn't start out viewing her as a potential romantic relationship, but that would change as their training develops.)
2. Keeping the Secret (Clark/Chloe)
Let me preface this one by saying that for the first three years of the show, I hoped the series would end with Chloe moving to Metropolis and taking the pen name 'Lois Lane.'
This one would take place fairly early in the show's run. Something happens that forces Clark to reveal his powers to Chloe, which is a worst case scenario for him. Her desire for the truth will force her to publish his secret, right? When she doesn't, it creates a new connection between the two of them. Suddenly, Clark has a partner, someone he can turn to through the insanity of his life. He never realized just how much he needed something like that.
I'm really interested in the idea of exploring a partnership between the two of them. Chloe was always attracted to Clark, but Clark didn't see her that way. Perhaps sharing the secret and working together to protect the city is what it takes to change that.
3. In Another World (Clark/Tess)
I really like the idea of an alternate Smallville, one where Tess was the heiress to the Luthor fortune who was sent to Smallville to master her business skills. It is Tess who gets distracted while driving and hits young Clark Kent with her car. When the young man is unharmed by the impact, she starts to grow suspicious. Despite her hunger for knowledge, the two become friends, and years later, something more. That close connection encourages Clark to tell Tess the truth, letting his guard down around the daughter of the town's most hated man.
What would a world look like where Lionel Luthor's daughter ended up with the son of Jor-El? How would their destinies be shaped? And what would happen when Tess's brother Lex came looking to take over the family business? These are questions I would love to answer.