I love this mission! My favorite feature was the constant sound of battle and screams that kept going on just beyond the fog of war. The layout was really challenging, and the fact that it made me think without overwhelming me with spawned armies. Lotsa replay value here, as there is more than one route to beating this mission, all of them equally difficult. Good job! Some feedback:

When I took over the RC - the objective didn't change to "completed" - and when I took over the HQ I got
two mission objective screens, followed by the mission win screen - one, where you told the computer to display mission objectives (which showed the RC objective as incomplete) and the second, where it apparently realized the RC was in my posession, as well. (which showed the RC objective as complete) - you don't really need to display these screens, just let the mission:win trigger do it for you, and maybe include a mission-ending ecom.

Out of curiosity, why is it called Haunted Mesa? I definitely got the "haunted" feeling while playing it, but there was never a reason....

You did such a good job with the layout of this map, it seems a shame that there was never a reason for me to go to the bottom of the map (Although for those who haven't beaten it - it is possible to get there!) - especially since the hq and the rc were facing more towards the top. Maybe moving the rc to the bottom half of the base might help?

Okay, I really wanted to know how the mesa was haunted, and half expected to see cyan "ghosts" storming the base after I took over the RC and HQ - hey, maybe you could expand the mission triggers in the future to include just that - maybe the ghosts could be the free radicals killed in the massacre or the original aliens that built the Replicators. Or, maybe something else. Just a thought....
Overall, I really think this mission took alot of talent to design, and I look forward to seeing what else you come out with! This one's earned a permanent spot on my Zodiac!