I don't really get why 3 issues of lore building from a character who used to be (and thematically still is) a large part of the book is a bad idea. I mean, he's coming back with story that Superman will have to deal with anyway. Plus, there's a very strong chance that Clark will be present in the issues because Reis is still drawing the two issues, and Bendis all but confirmed that Brandon Peterson is doing the flashbacks alone, so it wouldn't surprise me to see the issues pepper in Clark and Jon talking in the present next to Jon flashing back. No idea the ratio, but reactions by Clark are all but assured I'd wager.
I'd honestly feel short changed if the son of Superman going off into space for a number of years wasn't given its multi issue flashback due. Regardless of how one feels about characters not named Clark, that'd be disingenuous.