@ Arthanor: Yeah, it always bothered me that the Surgery Room can't be used for healing. I'm not sure if having a separate role like 'Doctor' is necessary though. The way I'd probably work it is you'd have an interface for assigning Brainers to heal wounded Gals, as though you were assigning them to research; the more Brainers assigned to a wounded Gal, the faster she heals. Brainers assigned in this way obviously can't do research so that's your opportunity cost.
Maybe a summary of Merc's glaring advantages, then?
#1: Nigh-invincible armor against anything below laser-class weaponry, including gas weapons
#2: No heal time
#3: No barracks space
#4: Flying
#5: Can't get better night vision than his
#6: Main weapon can reliably destroy anything short of a tank or power armor (if you have the skill to use it)
#7: Offhand weapon can one-hit-stun anything short of power armor
#8: Generally superior to undeveloped gals
#9: Fearless, thus Psi less dangerous.
#10: Almost immune to own weapon, and high-end armors are immune to his weapon too, thus Psi less dangerous.
You say it's not worth it. I say maybe yes, maybe no. The goal behind introducing him is, thus, fulfilled. From practice, I've succesfully used 4 of them (backed by 8 swabbies and 2 veterans) to repel a Star God raid on my hideout. Nothing clears a corridor like a big guy with a big shotgun.
#1: Gals can get comparable (and better) armour.
#2: Yes, but you shouldn't be wracking up injuries in the first place outside of terrible RNG. The real advantage here is that they enable more aggressive/reckless play vs weak opponents.
#3: Minor benefit excepting production bases. As I said, they have exactly one (1) enduring niche, and that's on base defense... but since you're hitting them with a big maintenance cost without providing anything in return, that niche will be threatened.
#4: Gals can fly; not an exclusive benefit.
#5: Largely irrelevant (honestly, you are insane to not spam lighting everywhere on Night missions vs enemies that can actually harm you short of having NV on everyone that will see frontline combat), but it's possible to get comparable NV.
#6: The same is true with most of the weapons the Gals use, though they are also capable of fielding tank busters besides and can kill effectively at far longer ranges and without even needing LoS. This is not an actual pro.
#7: Gals can get things that do this.
#8: Sure.
#9: Fearlessness is nice but a small benefit in practice vs 50+ Bravery. Psi remains incredibly dangerous with these guys; that 38 VD STR with no skill is a big liability, especially when you consider how close they have to get to the action (and subsequently how much more powerful and likely to work MC becomes).
#10: Scale and even Plate can get rocked by this weapon; unless your dudes are all outfitted in power armour (in which case why the hell are you still using Commandos), the Boom Gun is dangerous to have turned on you.