One thing to consider is that they can easily scale down the stories after Apocalypse.
If they do decide to go bigger, they could take it into space (which would be great - imagine the Shi'ar landing as the end teaser of Apocalypse - and would suit Singer, as he was planning a Battlestar Galactica movie).
Or they go smaller and keep it terrestrial with threats like Arcade, Sinister, Mojo, Moses Magnum, Omega Red and Soviet Super Soldiers (the mutant ones like Darkstar), Friends of Humanity, Proteus, Purifiers, Reavers, Marauders, Morlocks, Cassandra Nova.
They could also easily mash together elements of the Savage Land (assuming that IP is with Marvel because of Ka-Zar), Genosha and Mojoworld to create some sort of crazy island with mutates, Sauron, dinosaurs (or dinosaur-like genetic experiments) and a ruler such as Sinister.
There is plenty of scope. It just needs imagination, planning and lots of inspiration from the classic comics!