It’s kind of fiddly and I haven’t used it much in play, but I do want to protect the kittens so here you go. I call it the “Gigantic” alien special ability: The alien is very, very big and only dies if you hit it very, very hard. Assign Threat Tokens to the encounter as usual, but put only a single Threat Token on the table to represent a single gigantic alien.
Now multiply the number of Threat Tokens in the encounter by the number of players. The gigantic alien dies only if you inflict that many kills on it in a single round.
When it does go down, it counts as a single kill for whoever pulled the killing trigger, because quit whining, Trooper, a bug is just a bug. If you use a Strength and don’t manage to score enough kills to destroy it, your use of the Strength ends the encounter and removes the Threat Token but only drives the gigantic alien away. No kill for your record.
So if the encounter has five Threat Tokens and you have six players, they need to inflict 30 kills in a single round to kill the gigantic alien. If it’s six players and a tough 8-token encounter, they must hit it with 48 kills in a single round. That seems to work all right for your big Cloverfield-style aliens — it’ll be virtually impossible to kill it unless someone drops a TPK Bomb, and even then it’s iffy.
Not bad, but I doubt the “virtually impossible to kill” comment. It will die pretty quickly once the players have improved ECannons – which in my experience happens very quickly.
Also, TPK bombs inflict 1d100 Kills per marine at Close – could be a lot of kills there.