Harvest Red when the mission just tells you "This is your goal, here are some tools. Figure it out." I thought WOW, FINALLY a mission that assumes an IQ > 50 on the part of the player. It was really satisfying to make some choices, do some recon, and do it for yourself.
The warfare crud at the end was really disappointing. It could work on a long-term scale except warfare is just too cluttered with fast spawning trash and mindless ant-trails of suicide soldiers.