One problem you get in any kind of RTS and in 2aw in particular is blobbing. Blobbing is when you take a blob of units and hurl it at your opponent.
The problem I find with blobbing is that it requires no skill but usually works really well. The reason it works well is math. While your blob has full weapons and armor the enemey has just a single ship and does not stand a chance. The single ship usually dies very quickly without inflicting any kind of damage on the blob. You go onto the next ship and kill that - till the entire enemy fleet is wiped out.
Currently the only real counter to a blob is another blob.
I have been thinking up of several ways to combat blobbing. One is area of effect (AoE) damage. Basically weapons that shoot and hit an entire area of units at once. This would force players to think more about positioning. Should I blob the ships for maximum efficiency or should I move them apart to minimize AoE. Is the enemy using AoE ships? Now this is strategy! You need to scan space and know which units carry AoE weapons before you try blobbing.
Another very similar way is death explosions. When ship dies it can go off like an area of effect bomb. In SpringRTS, a feature it probably inherited from Total Annihilation is chain explosions. Basically if one puts building, turrets and even some units next to each other and one of them gets hit - all of them can go off via chain explosion. Where is your blob now?
A third option is to have units be big and have very short range and get in front of each other. This way all units in the blob cant engage the enemy at once. I dont see blocking/short range going well with 3d ship based game because naval ships shoot far and in 3d units dont block each other much.