Agreed, but I think the huge number of troops you were allowed in the original was meant to reflect just how easily they died. Have you noticed that fire in the new game is simply a hit/miss calculation? I've seen enemy shots miss their target and do no damage to anyone despite hitting my other squad members square in the face. Similarly the shot sometimes hits the target but is still a 'miss'. Oddly enough though, shots DO damage the environment that they hit (destroying walls and setting cars on fire) they just do no damage to any units other than the intended target.
The reason I mention this is to backup the above point that you died a lot more in the original! Shots could miss the intended Commie but still wipe out some poor sap stood behind him as could friendly fire. And lets be honest, even with power/flying armour in the original you were never going to survive more than 1 or 2 hits from an enemy weapon. In this remake you can suffer hits of only 2 or damage despite having over 20 health available to you so again harder to die.
That's why the original had so many soldiers and was unquestionably more of a cannon foddery undertaking. It's also the reason why (in my opinion) adding more soldiers to the squad size in this game would unbalance it somewhat. Sure sometimes you make an unlucky move and find yourself outnumbered but unless you're either really unlucky or really careless you should be able to fight your way out of it with the right tactics!
I know it's not always the case as I got a bitch of a mission one time where all of the enemies spawned right by each other so every move I made after discovering the first 3 mutons uncovered 3 more... I'm guessing that's kind of what happened to you Mickey is it? And I'm also assuming you mean 9 mutons altogether right??? Otherwise it's an insane battle if it's nine of each
Again though, I'd say 12 aliens is a pretty standard battle on any difficulty, the trick is how many you have to fight at once though, so if you're saying they all popped up together (like they did for me one time) then I agree entirely with what you're saying. But at the end of the day that's not normal gameplay, just REALLY bad luck!