I hope that's the case. I remember even PKJ having some choice words for how absurd Clark's treatment of Jon was, and how he felt all but assured that Jon would get powers too. Obviously he's not "in on" anything, but he's a writer, so it's at least noteworthy to me that he thinks it's a no brainer too.
The issue writers have found themselves in is that if Jon gets powers to at best it's redundant, and at worst it totally reverses the dynamic back to where they started where Jordan felt less than and Jon was exceptional because chances seem quite good that Jon wouldn't just be physically good with his powers given his 14 years of physical activity at a naturally high level, but he also wouldn't be such a selfish little baby about his powers since time and time again he's shown to be so selfless and about doing the right thing.
The only thing I could think of would be to make his powers even more unstable and dangerous than Jordan's. As in to the point where you're hard pressed to see them as powers and more of a legit affliction. Like, Jordan's powers are "unstable", but not really, right? They're unstable for a day or so and then he gets a hang of them. And his physical powers are at such a low level that he'd have to actually try a bit to really hurt or kill someone.
But if you make it so Jon's powers turn on and off at random (like he's not physical strong or durable all the time like Jordan is), do things like give him seizures like Tag, and make football impossible for him? Then the new dynamic between the boys stays there. Plus maybe Jordan's bum ass can finally start helping Jon out, and maybe Clark might actually go "oh snap, Lois, when did we get another kid!?" Jon would finally be able to really relate to Jordan's mental issues in a sense because this would mirror the uncontrollable outburst. Maybe Sam and John Henry create some sort of drug that helps regulate him, but he's gotta take it regularly. In a sense Jordan would be physically gifted one that would comfort and walk Jon through the bad times like Jon did for him.
You could even roll the Natasha plot in pretty nicely. In the episode Jon and Lois learned about Natasha and the other Earth, Jon seemed to long for a bond with her saying "I really wish I could've met you, sis". You take that and you have Nat start out just as hateful of Clark as John Henry was, but you now add in that she resents the boys for taking her mom. Then she sees how dangerous Jon's condition is, and relates that back to an evil Superman. Add on the fact that Jon was forming a bond with her dad, and she'd be at odd with him in a dramatic way that is driven by his actions and character.
Plus, because of his powers being basically unusable...*sigh* you can still have him shoot your stupid guns when he's in danger or he wants to help. And you only have lucky flashes of him using his unstable powers to help so that Jordan's status as the kid with powers is left mostly intact. I think this would fit with the themes and ideas of the show.