I agree with Iscariot that zone control goes to the hi-tech ships. Utterly. However, while I recognize how that works in the current version, I don't think it will mean as much later down the road.
You see, zoning out your enemy is fine, and should force a retreat for obvious reasons, but you haven't defeated anything. All you've done is fight them to a stand still. If the AI acted in a more rational manner (it's getting better for sure), when you zone out a large fleet, they should retreat, and then attempt to fight you again, but with more caution put toward protecting at least one capture point.
Really, this may be a bit of wishful thinking, but I'd like to see the larger game NOT focus on zone control more than is absolutely required. Mainly because it's a really easy exploit for the player to take advantage of, as it has been in every game that included such things. (thinking of SW empires at war here) In any case, my point is that zone control is not an end in itself, defeating the enemy is the END, zone control is just one of many ways to get there. Currently, a slightly unbalanced one at that. (obviously, it's an Alpha and allowances are made, just speaking as to the current state of affairs)