So far my biggest dislike is the comrades rules. I am not against such rules or anything, but I find them to be a bit of a cop out. For example, the Commissar's Summary Execution ability allows him to kill a NPC (Comrade) when a PC is severely injured to let the PC continue and to ignore his injuries until the end of the encounter.
It makes no sense. "Ah hell, Jennings stepped on a land mine!" Says the Commissar turing to CPL NPC Bouregard as he draws his bolt pistol. BANG! "Get up Jennings!" So as a Commissar I kill a perfectly healthy guradsman because another guardsman gets serious injured? I rather it work to increase morale because the commissar is allowed to kill you if you run. Such as a +10 or +20 to Fear/Terror/Whaterver checks as long as the Commissar also makes his or her check and have the bonus extend to everyone in the immediate area of the commissar because HE IS ALLOWED TO KILL Y OU. I mean what happens if only 2 PCs are left? Does the commissar kill one of them? Kill himself?
Maybe base it more on the wargame, with Stubborn (no penalty to fear/morale checks when lead by a commissar) or even oldschool 3E 40K version (which included summary execution and gave a +1 LD bonus).
As a Commissar serving the front lines in the wars against the enemies of the Imperium, you carry the authority to execute those found wanting. Whenever you are present when a NPC or PC in the Imperial Guard fails a Willpower test against or any other variaiton of morale in combat you can make an immediate reaction Intimidation test. If you succeed the target is permitted to retake the Willpower test with a bonus of +10 per degree of success you recieved on your intimidation test. If they PC or NPC fails the second time you immediately shoot him or her at point blank range with an automatic head shot.