Just beat the game for the first time yesterday (you can read my list of post-campaign quandaries here:
https://openxcom.org/forum/index.php/topic,4352.0.html). My experience was the same as others above. MC made it pathetically easy to get to the brain room and destroy it. I lost one soldier on the surface and none in the base. The whole thing was just anti-climatic and unsatisfying.
So then to mix it up, I reloaded a fresh Cydonia map, but this time I didn't use any psi-amps and I brought along some of my oldest soldiers who had low bravery/psi strength, so didn't make the cut for my first Cydonia mission. The result was much more of a challenge and way more fun.
Naturally, I started by sending my mentally weak cowards out to scout and of course, one of them (10 psi strength) was taken over on the first alien turn. I knew going in that Captain Timothy McCahery (named for my cousin) was going to be a liability, so I equipped him with a laser rifle and smoke grenades. Laser rifles are relatively ineffective against flying suits, but still can deal with aliens just fine. However, even flying suits have their laser limits and apparently taking six shots to the face from your teammate at point blank range is over the line. Hence, RIP Sergeant Link (of Zelda).
So after that friendly fire, the added challenge was to not only kill the aliens and make my way to the green lift, but to sneak around Timothy and avoid getting too much of his reaction fire. My squad stepped up big time, had some epic long range kills with their last snap shot and slowly, but surely we fought back. I lost three more soldiers (RIP Sergeant Mario [of Nintendo], Sergeant Donatello [the Ninja Turtle, not the artist], and Sergeant Neelix [of Star Trek Voyager]), but eventually we had everyone in the landing area ... except Timothy. I got control of him for one turn, disarmed him and moved him close to the lift, but then he kept panicking and there was still at least one alien out there doing mind attacks (how many aliens they had left, I don't know).
I know most commanders would have just left Timothy behind, but I couldn't do that. He was from one of my earliest batches of soldiers and the original "defacto leader" back when it was just one base and 14 troops (he was the first Captain, but was never promoted afterwards for obvious reasons). Plus, he's my cousin and Christmas would be awkward if I just left him to die on Mars.
So thankfully I had equipped one of my other mental weaklings with a small launcher just in case he went mental and after two direct hits, Timothy was unconscious. It took four soldiers to drag his sorry ass and all his equipment into the landing area, but we got him in there in one turn. I also had to revive him before we entered the base because for some silly reason (a definite oversight on the game's programming IMO) the Cydonia lift doesn't recognize unconscious soldiers when you hit the "abort mission" button. I think if it's on the lift it should go down into the base with you, but whatever, we got the job done and saved Timothy's life.
The decision to rescue Timothy ended up being a clutch call on my part because once in the base he was the main focus for the Ethereal mind attacks. Sure, they took control of him almost immediately, but this time I only gave him a small launcher so worst case he might knock someone out. Using him as a "psi-rod" probably prevented some of my other troops (two of them were in the 20s for psi strength) from succumbing to MC. There was one really scary moment though when Timothy shot a stun bomb out of the darkness and I thought it was a blaster bomb from an alien. Big time relief when it just hit the wall harmlessly.
Once inside the base my guys were pretty efficient in clearing it out. There were a couple nail biters when a Chrysalid charged out of the darkness at my troops, but some solid reaction fire from Captain Robert Johnson (my boss) and Sergeant Chewy (of Star Wars) saved anyone from becoming a Zombie.
We were down to just the final hallway and one Ethereal and hadn't lost any men in the base. But someone had to be the guy to go down the hallway first and that's how Captain Daryl Dixon (of The Walking Dead) was "naded" to death by the Ethereal who
jumped ... err, floated down.
After that, it just took some shots from the door by Colonel Princess Peach (Nintendo) and Colonel Coach Underwood (my former coach) to avenge Daryl by killing the final Ethereal (who was also the final alien alive) and finish the game off without even having to go into the brain room.
So that's the story. Some of the final challenge was self-imposed, but overall it made for a much more "epic victory".