I am not familiar with the character Apocalypse but I read now that he kinda was the first mutant back in ancient Egypt, so I don't think Wolverine's time traveling had anything to do with triggering the post-credits scene per se.

I'd say in the end it depends on the creator's casting calls and who they get to sign up for it all. They could set it in the 80s with the First Class characters that are still alive (pretty mean how those who died in the experiments remain dead even in the new timeline). Or in the 2014 X-school present with pretty much everyone back but in their older versions.
I am not sure if they had Cyclops or Jean Grey for example sign up for anything beyond their surprise cameos here. We'll see. Anything goes, which is very exciting.