From what I've seen so far, the "meta" is:
On navy, balloon armor and speedboat attack are the most important upgrades.
On land, it differs, but mostly I've seen people going for balanced gyro upgrades, with a little bit of armor on the balloons.
And that's because waving is still the best fighting tactic for large-scale wars, allowing you to destroy the most generals in the shortest amount of time.
Of course, people also upgrade swordsmen (evenly), hoplites (evenly, with a bit more armor), carabineers (attack only), mortars, and rams. The same applies on the navy side.
But if you look at how they spent their crystal (on navy; land is a different story), you'll find that about 75% of it went toward the balloon/speedboat upgrades I mentioned, and 25% went toward all the other ship upgrades. Hence, you can tell how important those two upgrades alone are.