What if Jon Kent is simply the first Superboy to join the Legion and Clark joins later when they are a bit more experienced? The Legion as currently depicted doesn't seem to be as far along in their teams development as usually depicted. Who's to say that Superman didn't recognize them because of a mental block from Saturn Girl or something? Or perhaps that was retconned by events in Doomsday Clock?
What do you all think? Would this work? I really want Clark Kent as Superboy in the Legion. Imagine Jon getting to meet his dad in the future as a younger, more inexperienced and brash kid. Wouldn't that be great?