What I've found with campaigns is that the requirements of the game must come first, with as much lore being crammed in as possible without compromising those requirements.
So for instance, you need a rigid structure to the campaign to prevent it drawing out for too long (and players losing interest as it goes).
No one wants to play one-sided slaughter-fests, so you don't want to engineer situations where one player has to come in, deploy, play a game (and give up his afternoon off to do so) just to play a match where he is outnumbered four to one, or otherwise so outclassed that the match is a foregone conclusion.
You want to avoid situations where one player has to play lots of games, while others don't play any. Studio Tomahawk recently released their Age of the Wolf campaign book, and one of the things I don't like about it is that players choose who they want to fight at the start of each round, with no limitations. Which might mean that all players decide to attack Fred, while Jim and Tony choose to defend and don't get to play any games at all this turn. You don't want someone to feel victimised, nor do you want someone to feel ignored.
Some things you could do for Armada might be to have your Admiral attached to a particular ship in a particular fleet. If another element of your fleet is engaged, then your admiral can't take part (and you will have no admiral for that battle) because he is elsewhere. Ships could start with no upgrades, and only be awarded them after fighting battles, and there could be an element of resource management to repair damaged ships. Titles might be one-use-only, with the title being lost after that ship is destroyed.