All the expansions are technically independent, but ZM and CoP are much more closely tied than any of the others. While you can do both in any order, you'll understand a lot more if you do Zilart first (at least up to Sky access).
Fortunately the Zilart line itself doesn't have nearly as much content (and no built-in wait periods), so you can knock out the entire mission sequence in a few hours with the same group if everyone is competent.
WHM90 BLU90 BLM90 PLD90
Midgardsormr -> Quetzalcoatl