In my experience Bendis needs 60-sum issues to establish a book's proper setting, character relationships, and ongoing momentum with his decompressed writing style. That's the only point where I could conceivably seeing a time skip not coming as out of the blue.
I guess it could give him the opportunity to jump to certain character points he wants to get to without needing to deal with the nitty gritty of actually developing them over time, but that's not ideal for me.
Jon's mostly in the future now so I'm not sure if that should impact Conner being Superboy in the present-day...I mean, if we're talking age-wise, Barbara Gordon is a 21 year old Batgirl, although who knows if the new timeline will finally make her Oracle again. Heck, cartoon Conner is getting married and still calling himself Superboy .
Plus Jon now seems set to jump to being Superman, so I guess Conner might keep Superboy by process of elimination.
I may be biased because I didn't really enjoy Priest's run (Jessica and Bruce wuh...?) but I don't know if he would be a good choice to start off a brand new Justice League unless they're, like, more Authority-esque.
I also wonder if he would be more open to writing less developed and established Justice League vs. "the main ones," since while that would be creatively freeing, he might prefer getting to write the more traditional and prominent versions.