Putting the JSA back on Earth-Two, and giving them a book with an Earth-Two bullet or masthead is about the best way to go for them.
And between Robinson, Goyer and Johns, they created the best legacy versions these characters ever had. So I'd hate to lose any of them. At the same time, it's time to separate the JSA from WW2. Seriously, I don't know why people think they belong in that time. On the DC forums, someone called it their "golden years" or "greatest moment".....
Why?
Unlike their Marvel Golden Age counteparts, they did NOT fight in WW2. They were sidelined from doing anything of real consequence and were relegated to fighting the occasional spy or saboteur...as well as doing charity gigs for War Bonds. The Spear Of Destiny cockblocked them from having their "greatest moment".
And personally I've always found that annoying. So I'm mixed....I'd hate to lose the legacy versions of Hourman, Stargirl, Jesse Quick and especially Starman....but I think I'd like the original JSA to be more contemporary.
On nuEarth, the superheroes will have been around for five years. I say on Earth-Two say the heroes have been around for ten years. That would allow for some of the legacies, though maybe not all.
And that's assuming that we have to continue with the idea that the JSA must be older for some reason. Really, at this point, there's no reason that that should even be the case anymore. They could just as easily have only been around for five years, if you want a really fresh coat of paint on them.
If it were really well done, I think I'd be okay with that as well.