So I'm sitting here musing on weegee's Unmapped Lands and the Metagame, and it occurs to me that 'kill the brain to conquer the site' is fine and all, but why not have other mission types you can deploy on later? For example;

1) Launch an attack before a transport arrives to pick up a gold shipment... so you can steal the shipment for yourself. This puts you under time pressure, as you have only a few minutes before they start loading the shipment into a transport craft. If the AI launches a raid against you, then you have to hold out until your shipment can be loaded aboard your own craft and launched, or kill all the attackers.

2) Raid a site for more intelligence on the enemy's other bases; get into the base, hack their computers, grab the files/disk/whatever, then extract... whilst reinforcements pour in to try and stop you from escaping, of course. If successful, this would reveal a significant amount of the map on all sites owned by the team you raided.

As for #2, it sounds a little bit like the zombie "chip" mission, IIRC something similar happens, I love those scripted missions. I will love if they implement these two ideas you are giving and even more scripted missions. The game is looking neat so far, is just a matter of time to get more cool stuff implemented.