I'd like to see on the Strategic Level, Resources. It gives targets to attack and defend. If you can't beat the big blue plague straight up, start knocking out Dilithium and Duranium Mines. Focus on Anti-matter production facilities, chip them away piece by piece. Once you've got the fleet spread thin defending all the resources, strike at a shipyard.
Another thing I'd like to see is Order of Battles. Yes, I am very much someone who likes the Strategic and Logistical side of things. But I don't think its very fun with everyone flying around in Battleships. And while I don't want to see heavier ships reserved for those who spent the most time grinding, I think there needs to be a limit as to how many Battlecruisers and Battleships are flying around. An easy way to do it is to have them be built, have each side start with so many of each type of ship yard.
Light Yard: Builds Frigate and Destroyers
Medium Yard: Builds Cruisers (Light, Medium, Heavy)
Heavy Yard: Builds Dreadnoughts (Heavy Battle Cruisers)
Huge Yard: Builds Battleships
More yards can be built as the game progresses, but if a race just builds Huge Yards, with the time and resources a race spent on just one Battleship, they could have built a half dozen cruisers. One Battleship would own the sector that it's sitting in, but six cruisers could put pressure on three or more sectors. And what about that attack wing of a dozen destroyers? One of the things we're going to have is that the Battleship is not going to be the king of a battle anymore. There's no arbitrary (6) player limitation so, in theory (and this would be awesome btw), every player online could participate in the same battle at the same time. I would imagine that a Battleship would be a prime target in such a battle.
One thing that the game is probably going to need, is a solid fleet control interface. It would be hard to find someone willing to fly one destroyer in an attack wing, but with a good fleet control interface, one person could control the entire wing from one ship, making them almost as powerful as that one Battleship. Maybe more so, although I would imagine that the Battleship should be able to easily kill each individual destroyer, the question would be if it could kill or cripple them fast enough to keep itself from being overwhelmed.