Ichoran made some really excellent points about how to counter some of these issues, depending on how or when it needs to be done.
Something my players seem to frequently forget is the common sense rule. Anything that you have as a player character, the enemy may also have. In fact, they may well have access to better goods because of who they work for. You drop them into a hot zone? It's hot for a reason. Arm the NPCs with anti-vehicular rounds. That gives them a leg up against anything your players are piloting AND halves their own armor if they get shot.
Oh, but magic- Magic I love. Your team is assaulting an established/entrenched force? Make sure the enemy force has initiates on their side, who've used their heads and prepared to defend. If they've been there long enough, depending on what they're doing, maybe the area has generated a background count that's beneficial to the home team and not the PCs.
Establish vantage points, like the old lighthouse that overlooks the field, or the top-floor rooms of buildings in the area. Put one or more enemy magicians there who have some manner of optical zoom, so they can observe the battlefield without any real penalties.
- Standard visual/aural check: Counter with Invisibility/Silence, or
- Team is doing thermo checks: Have the rooms insulated.
- Team uses drones/vehicle sensors: Make it Improved Invis/Physical
- PC Mage peeks at the astral, to check for spirits or invisible
magicians: Counter this by having your opposition inside a warded
area, but make it a masking ward, so from the outside everything
appears mundane and normal.
- PC Mage decides he's going to scout from a great distance out:
Defending team established perimeter alarm wards, they're harder to
detect the stronger they are. To add to the sneakiness factor, make
it a triple ring of wards. The outermost layer is only rating 2 to 4.
Middile ring 5 to 8. Core ring 10+. They've been here a while, they
can all pool their talents to make these wards.
- Team mage starts getting mana-bolt happy: Make sure the defense has
shielding, that'll increase the PCs target numbers. Combine it with
Reflecting, your PC is potentially hurting himself. Use Absorption
instead, the enemy eats the power thrown at him and uses it to hurt
the PCs, or do whatever else he wants with the mana.
- Is your PC magician being extremely offense-focused once the fracas
begins? Have the enemy hit him with something nastily debilitating
at a goodly force and then quicken it on the PC. Obvious things are
attribute lowering spells, but maybe your NPCs like to slam people
with Slow Death (Src: Target: Awakened Lands) or their own custom
offensive health spells designed to inflict diseases, or allergies
against what the local mundane troops will be using to try and harm
them. The PC may wind up taking so much extra damage due to the
allergy issue that they can't even focus to perform magical deeds at
that point. In extreme cases, throw something at them that will
drain their essence.
- Team wants to use spirits of their own: Make sure one of the
opposition is talented Shamanist or aspected Conjurer. (no need to
keep using full magicians, they're more rare and expensive). Give
the defenders decent power or spirit foci. Masking will let them
hide their own magical nature (and their foci), so they could be out
on patrol with regular troops. If they're able to use dice for
spell defense, let them also learn Absorption, Reflecting, or
Shielding. As specialists in spirits, make sure they have Invoking,
so they can call down great form spirits if they wish. Give one of
them Channeling and that great form spirit can suddenly be something
that makes your NPC faster, stronger, tougher, and immune to mundane
weaponry. If this enemy force has been there a while, they may well
have multiple spirits prepared to begin with, so they won't get
knocked out in the heat of battle, and there's nothing that gives
away who the controlling magician might be. Let them use the
Movement power of a great-form to make everybody among the enemy
forces move faster.
- Maybe your team is stealthy and lucky, but they decide to quietly
geek one of the sentries guarding the area. You've got magical
talent on the scene. Make part of the security sweep involve using
Sensing(also Target: Awakened Lands) to monitor the astral terrain
and phenomena. A new spike in the background count from a murder
happening may catch their focus. That could be worth re-positioning a
defending strike squad and put them on high alert.
Something I've only used once, just for the big FU factor of it, I put together a small squad of complete mundanes who were jungle tactics specialists, but each one carried a magical anchor designed to activate automatically if they ever received enough damage to hit deadly or beyond. They get hit, they fall over seemingly 'dead'. Most PCs immediately change their focus of attention when they see an enemy drop because there are other threats, meanwhile NPC #3 is being hit with a high-force healing spell that has no visible special effect or source. While backs are turned, maybe he decides it's time to use his grenade launcher.
When all else fails, if you are for some reason of the "I don't want to kill my players" mentality- hey, that's fine. Don't kill them. Maim them. Cripple them. Blow off limbs. Magical healing doesn't fix an arm that's been turned into mushy pasta and spread across a dozen meters of terrain. Use the Wound Effects and Permanent Wounds caused by the trauma they're taking on the job. You can (almost) always get a replacement leg, if you can get back to a safe harbor, but Attribute losses (page 128, SR3 core rules) aren't just permanent, they lower your racially modified attribute maximums.
Your crew won't be dead, but enough losses that they simply can't recover via new and improved 'ware, and through zero amount of physical or mental training, and they may discover they just need to be retired, they are no longer at the top of their game. This could potentially open up avenues for them to escape their corporate overlords, who don't see them as worth the investment any longer, which also gets rid of their sources of goodies. If they survive their attempt at running and somehow don't get their brains pasted, then it's a whole new life of trying to get rid of everything the corp put in them, to disappear.
Look at the various locations there is good game material for, or invent your own. Their only way out may require submerging themselves into entirely new environments where they just haven't developed the adequate skills, and they'll probably have zero connections. You don't have to kill them, but you can beat them down enough that they'll be back at low-tier runner levels, and still able to have some fun with their new 'freedom'.