I like everything Ascended and mos1979 said with the two changes: I'd have Martha the parent to die when Clark is young. Switch it up a little. I prefer them both gone but as a compromise. She becomes ill sometime after high school (with the car accident scenario being removed in a huge Vyndktvx storyline which serves as the rationalization of the changes), and passes when Clark is in college. After this Clark takes a sabbatical from school, and does lots of travelling (he gets that Birthright/American Alien world experience here). Play on a somewhat strained relationship with Jonathan as they both try to deal with losing her, but they eventually patch things up completely early into his career as Superman and become close as ever.
Secondly, Clark and Lois would not be married. I'd establish a firm past with a romantic element, say they've been intimate at least once and although neither regrets it, they've still decided to hold off on anything serious for a variety of reasons. Jon doesn't exist at all. Conner Kent is Superboy and he is of course the Karl Kessel version. I like the kid but he's a bigger problem than he's worth continuity-wise. Its not worth it yet. Save an idea like that in your back pocket in case you decide to marry off Lois and Clark again in the future and introduce a son organically. Again its no problem with Jon inherently. There's nothing wrong with him. Its all about how he was introduced and how he exists currently. It was rushed, hackneyed, and requires huge accommodations to the crafting of an overall mythos for Superman that just is so not earned at this point.