I'm sure there will be some of this. Like habits, traditions, or even points of view that he forms from his time up there with Jor-El, but remember Bendis said that the first thing Jon says when he gets back home is "grandpa's crazy!" So, likely not the mini Jor-El that some are assuming. Even the choice in saying "grandpa" over "grandfather" or whatever seems to denote at least a base of old Jon is very much there.
I think the main points of friction will be 1) Jon's appearance. I'm pretty much convinced that he'll be showing up in that gangly post-puberty body we were teased, and that's gonna really hit Clark hard because he's gonna feel like he missed out on his boy growing. 2) Jon's technically an adult by Krytonian standards, and he's probably taken that more to heart than his parents understand/assume 3) Doubt he's ever going back to normal school. 4) This is probably gonna be a big one: I doubt he's gonna keep a secret identity any longer. Aka glasses aren't likely. Basically, Clark's dealing with both a kid becoming a teenager AND and kid coming back from super space college. Bendis probably channeling his own personal experiences and seeing it from the other side with his oldest child.