Never said I had to pick one. I love Jon as a character and I'm totally unashamed of it. I'm only conflicted because of the idea you put forth: Jon being the son of Superman possibly putting Jon in a Lina sort of position. I'm only conflicted if this theory holds true, but even if it holds true and Kon is gone because of Jon, I'll continue to love the kid.
You can look it up yourself. The creators of the show already expressed that they wanted to do another time skip. Given the popularity of both Jon and Damian (Damian not only getting a spot in the new Injustice game but also getting his own Batman solo game), I wouldn't at all be surprised if they wanted to use them.
That's the thing we just don't know. They could very well just be putting out those old stories in the interest of swelling up focus on the Superboy brand and not specifically the character of Kon.
Have you ever checked out Young Avengers by Kieron Gillen? It was probably the best new superhero book of 2013, honestly. Well there's this character in their call Marvel Boy aka Noh-Varr. He's easily one of my favorite characters in comics, and part of that reason is because some of the way he's written by Gillen reminds me of like a cross between 90s Kon and YJ (show) Kon. He's sexually active/charged and not at all shy to show it (
https://s-media-cache-ak0.pinimg.com...3f6879bd71.jpg). Look at how dope and effective he looks in action (
http://wac.450f.edgecastcdn.net/8045...1372032499.jpg) I think if they took a little inspiration from Noh-Varr, Kon would be in a very good and distinctive place. Jon can be cute, wholesome, and infectiously charming. Kon can be sexy, cool, and free loving. He'd be the sex symbol of the Superman family. Somewhat like Dick Grayson.
I could easily see Kon saying something like this