How about a Karma system like with not killing the seintists only with gaurds to. Being able to capture human enemys instead of killing them. Also would be cool if you could calm certain test subjects down and let them follow you for a short time. when time is up they would either get killed or find a way to escape the lab.
Ok so far it looks ridiculously epic. The whole sword thing was a bit unexpected, as we are used to grabing a head to rip it off, but I think it's pretty good so far. Now the questions (I can only do 1 cause of text limit): 1. Co-op would be an enjoyable gameplay system, however as you said it would hinder the thermo. I think that if you add co-op it should be shortened to only 2 player. Now an intresting thought would be that you can, if your up to it, make a 4-player TS Battle "Game" in addition to TFD.
My suggestions r 3, 1-4 player Co Op 2- you should be able to free other civilians who are about to go through the changing proccess and have them follow you till death 3- you should be able to mug the guards and stuff to take their uniform as a disguise >:D