Why not a combination of both the old zone based system and the new CP per continent system?
In addition to per region "difficulty adders" (often lumped into areas of the same number, like before), but also have each region get tougher upon every civilization tier, though possibility at different rates. (Like higher level regions get more "goodies" in terms of enemy types, new enemy behaviors, and to a lesser degree, enemy stat bonuses, faster per tier than lower level regions) This would give an interesting dynamic. Should I rush the high tier regions early, before civ tier goes up, but I have far less tools and upgrades to work with, but possibly get more rewards per mission/area/enemy earlier if I do survive? Or should I play a more "standard" progression and play up through the regions, and thus have more tools by the time I reach the high tier areas and overload areas, but they may have gotten more awesome stuff to work with as well?
Again, with their being a tier cap, this sort of system is feasible now, where previously (with no tier cap) it wouldn't be.