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My favourite counter against big troll adepts is a small army of grunts with shock weapons. The sheer number will help bring his defense dice pool down and the electrical effect is usually a weak spot. If he happens to not wear chemcal seal, neurostun and the like take him down easily.
Of course baiting them into a BC of 2-3 (with a domain in your favor, if you were awakened) will cripple them fast.

In Shadowrun, a simple physical combat is rarely a challenge for the PCs. It will usually go like this:
PC1: "I spend Edge to act first, I shoot him with Edge. 24 hits."

Then either the NPC dies or the GM spends Edge as well, until the NPC is out of Edge. Since he has less Edge than the whole team put together, there will be at least one PC with enough Edge left to shoot him dead.

One solution is to bring the PC to the fight with no Edge left, but that doesn't solve the problem that the PC will act far more often than the NPC. You can arrange things to get a one on one, but then it's no fun for the rest of the PCs.

So far, the best way I've seen was to challenge PCs in a different way. For example, they had to get a twisted mage who loved mental manipulation spells. He had a group of "servants" who were just SINless who served him because of some mind manipulation and a lot of fear. He lived at the top of an old 20 stories building (his "mage tower"), and the PC had to get him alive. The servants let them enter the building and start going up a few stories (with the stairs, since the elevator were broken) before following them. While the PCs were climbing the many stairs, the mage cast spells at them using a fiber optic network built in the stairs for that purpose. He mostly toyed with the PC, making them suspect traps where there weren't any, making them bump into each other, and so on. When they finally arrived at the top of the tower, the mage had shapechanged into a crow, in the middle of the whole murder of crows that was there, his aura hidden by both the background count and the crows. He then had fun with the PCs, masking one of them as himself, making them feel as if the crows were mocking them and so on.

Otherwise my favorite BBG is someone who fight socially. Someone who's loved by everyone so that killing him would destroy the PC's reputation, someone who's able to trick PCs into doing his dirty work...

Are you looking for advice or someone to give you an example BBG? if you want a good possible BBG, a IG 5 Mage with a few lower grade Mages/Adepts that make up his Mage Group. maybe the BBG, a second in command & a couple of base Mages/Adepts from the book as mooks, if you're looking for an example of what the BBG might look like you'll need to give a bit more in the way of details so as to prevent anyone from creating an overpowered monster (which many dumpshockers can do quite easily)

If he really hates trolls, he might have the slay troll spell. Demolish guns is also an effective opening salvo for a mage. It disarms the opposition and you don't need to blast it at a particularly strong force depending on how you handle damaging weapons. If the mage counterspelling is going to be an issue, you could always open with a salvo of grenades. And if the mage ambushes them, have it be from behind armored glass. It means that the physical adept can't just charge and end the fight, while the mages can duke it out magically for a little bit. Also, physical mask on some armored attack drones can really mess with the parties head, especially since the mage will kick themselves for not going astral to check it out. "What do you mean he's still conscious after two stun balls and a burst of SnS? What the hell is this guy? I thought you said he was just wearing a bullet proof vest." Ford LEBD-1 + 10 armor mod 6,500 nuyen. Just one option.
"A flying dwarf? What the hell, how many mages are here?" MCT- Roto Drone with physical mask.
They aren't actually hard to beat, the group will just frequently throw the wrong things at them making them a challenge and then adding to the suspicion on anything else they encounter while going after the mage.