
Design
Now, lets define the 'Soze' type enemy, shall we? This is my perspective, YMMV. Note: For the purposes of this exercise, 'Mr. Soze' is not a Great Dragon, an Immortal Elf, a free possession spirit, nor any other absurdly powerful individual. He's just a guy (mage, hacker, etc.), with serious connections and an anonymity fetish.
Due to the extensive and pervasive nature of 'Mr. Soze's' influence I intend to create him as an organization, rather than an individual, consisting of 'Mr. Soze', 'Mr. Kobayashi', and an undetermined (but relatively small) number of trusted prime runners/minions, henceforth known as KSO (The Keyser Soze Organization). All others will be referred to as 'puppets'. Puppets will not be rated here as they must be dealt with on an individual basis.
Group Connection
Adjust as needed for your purposes.
Membership: +1 (2-19 members worldwide)
You'll rarely, if ever, meet members of this group. Most of the PCs dealings should be with unknowing puppets.
Area of Influence: +6 (Global)
Cuz, ya know, it is.

Magical Resources: +2
Though this is not really a valid number by RAW, KSO is likely smart enough to recruit at least one high-level initiate, and probably several very talented adepts, and the Raw +1 for 'a few members who have knacks, minor talents, or very low ratings' (RC p.124 Magical Resources) doesn't really cover it, so, +2, for at least one high level initiate.
Matrix Resources: +2 (Broad reaching resources)
See Magical Resources and substitute 'highly-skilled hacker' for 'high-level initiate'.
Total Group Connection Rating: 11
(Note: Adding in the Puppets would likely increase all these numbers to 6+, so, if you must, consider the effective total organization Rating: 25, which gives you 25BP, the RAW maximum for the Enemy Negative Quality.)
Incidence Rating
This you will have to adjust for your own game. Are you just an annoying fly they occasionally try to swat? Or, are they hunting you down like dogs? Are they an inconvenience to you, or, are you the one driving them nuts?
I'd suggest setting the Incidence Rating as normal, depending on what your game needs. At Ratings 1-4 your PCs should only deal with, or confront, puppets. Only once they've reached Rating 5 (Foe) should they encounter KSO members, and then, only peripherally. At Rating 6 (Nemesis), feel free to send KSO prime runners after the PCs directly. 'Mr. Soze' should be kept away from the PCs unless he's 'undercover' or he's the only one left.
Implementation
As there are likely innumerable ways to use this particular enemy, I'm just going to mention a few here. Please expand on this in your own posts. Note: The KSO work through fixers, 'Mr. Kobayashi' not being one of them, until you've really fucked up that is. 'Mr. Soze' is the puppet master and no one outside KSO should meet him, at least, not that they're aware of. Intermediaries should be the norm.
Former KSO Members:
The PCs were once members of KSO, but, due to a failure to perform, personal disagreement, discovering a "deep dark secret", or just outliving their usefulness, they are now hunted (add Hunted Negative Quality as well) by the KSO, or, at least inconvenienced by them at every turn.
No one retires from the KSO, a.k.a. 'Kill Keyser': (A variation on Former KSO Members... a la 'Kill Bill')
After cutting all ties with the KSO and disappearing into the shadows, they come for you. Murdering your family, destroying all you love and mistakenly leaving you for dead, they've created they're own worst nightmare, a shadowrunner with nothing to live for, except... to kill Keyser. But, first you gotta find him, good luck with that. (Add Vendetta Negative Quality, possibly Lost Loved One as well, if they took your kid.)
"You Have Stolen From Mr. Soze":
Having unknowingly run against KSO assets on one or several occasions, the PCs have been given an opportunity to 'redeem' themselves. The questions in your mind are, will you survive the suicide mission, and if you do, will they let you live afterward?
Loose Ends:
Having been used as puppets by the KSO one too many times, the PCs have put together the truth about 'Mr. Kobayashi's' employer. The KSO cannot let them continue to breathe, after all, they may talk in their sleep...
Competition: (Pre-KSO Keyser Soze)
Dealing with a drug-dealing punk should be easy, right? But when that 'punk' shows you the true meaning of Willpower, will you survive? Your contacts are dropping like flies, your family and friends are all dead, can you outsmart him before your time runs out?
Convert from Group Connection to Individual. Stat out 'Soze' with maxed Mental Attributes, Exceptional Attribute: Willpower, and maxed Edge (try really hard to keep Soze alive), probably a Sam or Adept, though a Mage might be good, also. Give 'Soze' the Vendetta Negative Quality.
Resolution
The end game. Win or lose, you're about to decide your destiny.
Losing:
There's only one way to lose this game, die. The question is, will you take them with you?
Winning:
Wiping out the KSO, or convincingly faking your death seem the most likely routes to me, though the Players will probably find another way.
In the unlikely event that the PCs have beaten KSO (i.e. either they're really good, or you fucked up, hopefully the former), you now find yourself with a group of surviving PCs that are probably really full of themselves. So, what are they going to so with their victory?
Hostile Takeover:
Well, they might become the KSO, that's a mighty big power vacuum to fill. This could be done several ways. They could announce the 'change in management', or, they could just start running the show with 'Soze' becoming a 'position' like CEO, The Dread Pirate Roberts, or Merlin, sans the friendly transition, of course.
The Full Bank Account:
They may loot the organization and retire. After all, if you're the guys that took out the KSO, it's possible no one will want to mess with you, or pay your exorbitant prices.
Exit Stage Left:
They might even just walk away (

Whichever way they jump, try not to act surprised. Players get arrogant and insufferable when they know they've got you on the ropes. And remember, if they do win, you can always smile and say, "Wow, a run that turned out just like I planned it."
So, thoughts? Criticisms? Improvements? Embellishments? Screams of, "You're a fucking hack Tachi"? Come on, lets hear it.
In case any of you noticed, my writing kind of went downhill a little bit as I went along. Well, I had 6 shots of 151 during the hour I wrote and rewrote it, so, eat me.
