Ok, Chris, Keith, and I had a skype chat this morning and we figured out what we're going to do. And personally, I love this idea.
First, we're getting rid of unlocks for elite enemies. Gone.
Then, as CP goes up, there becomes an increasing chance of one of the elite enemies coming into play. They will never completely replace their lower down counter-part though. So, while the game might introduce Eagle Divers, there will still be regular eagles too. What enemies are introduced and the order they are introduced will be random.
Also, the randomization process gets reset each continent. So, you might see Skelebot Kneecappers in the first continent. In the second one, they might not be there, while the second one might have Repulsive Dust Storms instead that weren't on the first. What this means is that as we add more enemies and more elite enemies, each continent will be more and more unique from other continents in that world.