As soon as Jon was introduced in the show I figured this would happen. I figured the reason why Conner had weaker/less powers was because he was a clone and not because he was half Kryptonian.
It does beg the question of if they do plan on doing a time skip for season 5, or if they plan on maybe doing a bit of time travel and showing us future Jon with the Legion. Adding in so many meta kids and making a point to show that some of them have powers seems like set up.
Well, since Conner has gone public I have to imagine that him being Superman is on the table. It's also already known that he's a clone. You can play with the idea of the public looking down on Conner and his weaker powers (and half Lex genes) while fawning over the young teen Jon as Superboy with his great power. Then you could get into how Conner is always having to prove himself and deal with insults, while Jon has an unfair amount of pressure put on him very early. You could even have Conner "Black Canary" Jon and show him raw power isn't everything.
I think it could work pretty well.