There isn't much you can do to change Retrieve mode, due to it's speed, aside from making less rewarding like Richard is asking.
I would, however, offer an alternative: give different missions different weight.
Retrieve is a FAST mission, and, lorewise, it shouldn't give you much, as you're only keeping what you already had. Give it a lower base value, and that will make spamming it less rewarding.
Assault is a slower mission, but it is, lorewise, much more effective against the enemy. They are losing major amounts of resources, and plenty of materiél. That is important for your war effort. Give it more weight.
Survival is it's own beast, and I personally think it's a horrific waste of the name. It's a modified Assault, and I dislike it. You should be surviving for a time limit, or at least a wave limit, with progressively harder and harder enemy wave. Lorewise, you would be intercepting an enemy invasion fleet, ahead of your faction's main fleet. Victory would cut one of their assaults down to nothing, and would be useful for your side. Not as useful, so I would give it a moderate weight for war-score, but it should offer a higher war-chest, for a bounty on enemy ships killed.
This brings us to Defense, which I think should have the highest War-score reward. It rightfully should be a little slower, and rightfully should be challenging, but not as uselessly difficult as it is. A major invasion is being sent at this Geothermal plant. You are the only one's stopping it. That is huge. It should be one of the more difficult modes, and it's war-score reward should have much higher weight.
