If they are prepared for war, you need to give them hell. If the scenario/type of enemy allows for army-type-squads, a send in 7 to 12 guys in Guard Flak Armour and arm them with Krak Grenades (Pen:6; 2d10+4) and one of them even with a grenade launcher.
I would assign Armageddon- Patter Assault Rifles with Stubber ammo, too.
Trained Professionals: Allow them +2 Ini Bonus if the pc are a) on the defenses and b) your pc´s "Commander" does not pass an Ordinary Check on "Tacticae Imperialis". Don´t forget to give them BF to allow for “Mighty Shot” (and the added damage bonus).
If you are up against ugly mutants, make them really ugly. A brute with ST 48 and T: 48 that comes with Unnatural Strenght and Toughness should give your group at least some headaches. Give hime some scraps of patch armour (flakk 2) and heavy medivial helmet (primitive 5). Make him really big,so you can justify high amount of wounds (20 or 25; which was declared “human maximum” in “Ascension”). Give him "Fear 1", just for the case. And use WS of at least 36. Add "Crushing Blow". Put a chain axe in his hammy fist and we are talking 1d10+14//AP:2 damage “total” here, with the tearing quality.
Make sure his "friends" are with him, because he will not last long otherwise. A dozen mutants, a third of them throwing fire bombs (AP:6). Not for the damage. No matter how mad your pc are, they cannot simply stay still in fire. Even if the do not get damage, the fire eats up there air, a fatigue level per round they volunteer to stand inside the fire is totally alright!. If they move out, it is a chance for "Biggy" to close in.
Add a "wyrdling" somehwere who got "Weapon Jinx" and a Psi-Power of 2. Give him a decent willpower so he can "overbleed" and therefore cause 2 or three weapons to Jam. More time for biggy and friends. And will the pc spot him? He does not need to look different then the other mutants, a hard (-20) Test on “Forbidden Lore(Psyker or Mutants)” could do the trick, so. Add one to three hounds charging the pc. They deal with them or they "jump them". Even if there teeth can´t hurt them, a large dog jumping at you full speed is totally able to just send you flat on your beg (treat it as a take down if the characters do not pass Strength test). More wasted time for getting up. If they "shot them like the dogs they are", it is more fire distracted from biggy and the boys.
If you fight scum and cultists, the attention those “heavy gears snooping around” draw justify to put a “Judge Slayer” in the hands of a number of the guys they are after (not all of them, mind you!). That will at least help a little AND those things are neither rare nor all to expensive. So, go ahead and have every forth or so have them. Again, Firebombs are your friend so one would need to expect a fight to have them. Like, if you are up to go on a riot or to set an ambush or if you put some last-ditch affords into the arsenal to defend your hideout against the attackers
A point no GM ever seems to use (and sure no FFG mission so far): have the enemies TURN AND RUN! No, really. Hideouts have secret exits, perhaps. Plan one mission were the characters come to the lair, charge in and have and see half of the cultists/recidivist/what ever TURN AND RUN. Now have the characters run after them and give them instead of a “final fight showdown” a wild chase to capture as many of the cultists as possible. Be sure to prepare an environment, turns and tweeks, things that get in the way and give the characters a chance to follow. Have SOME “enemies” be mad, stupid or shocked enough to stand and fight for (another) round or two so the other get a head start. The characters might shot some down.
Weapon servitors are no bad choice, either. Heavy Stubbers are a good start, close combat servitors are, too.
And again...make sure to take the fact that the character is totting a towering shield along into the description of any scene. You do not need to pester him unnecessary, but FAIR AND SQUARE such things should make a difference. Even in the GRIMDARK40K.