Lois doesn't need to be a mother right now, and doesn't want to be a wife for the time being. Similarly, Clark has a reprieve from his role of a father – for an amount of time to still be determined – and is essentially living the life of an estranged husband in Lois' absence.
The lives the two are living now comprise the recipe for an eventual divorce.
For whatever reason, Superman tells Lois he likes the new "us." What's just as plausible as his willingness to happily go along with their separation is his possible consideration that their new "us" might not be as a union. Is Clark now pondering the possibility that he and Lois will soon be divorcing?
Is this the beginning of the end of the era featuring Superman as a family man? Serving the role of the world's greatest hero doesn't leave much time for family, after all. Lois, historically, has always been a reporter/writer. And Jon sounds like he might be quite content being raised by Grandpa as the pair travel the galaxy. Superman's never been closer to resuming the old status quo than he is right now.
Superman and Lois look to continue going their separate ways in Action Comics #1005, on sale November 28.