Again, all of the scaling happens ahead of the runs. The GM creates the world and defines the type of game you're going to be playing based upon varying degrees of input/feedback from the players prior to character creation. If people want to run mega-optimized/broken games, go for it. I personally don't find a huge power balance in favor of the PCs or NPCs all that fun in play. If others like it that way, go for it. I was in no way advocating for fudging dice rolls mid-stream or houseruling mid-session but I have no problem w/ a GM upping the challenge level of the opposition for the next session if their attempt at balancing the last session didn't quite hit the mark.
The GM should know in advance the general level of difficulty and security at every level of facility in the world; from a stuffer shack up to a Zero Zone. The Zero Zone might have high rating milspec matrix systems, dozens of high force nested wards, hundreds of high force spirits, every square millimeter under constant surveillance from all types of sensors, hundreds of guards in assault armor loaded down with enough high end combat ware that they are almost cyber zombies, and with a full suite of skill softs to ensure that in any potentially relevant skill they have at least 4 points from the soft.
But if players who are built and speced to survive running against such a Zero Zone decide instead to raid a local accounting firm, well that accounting firm is not suddenly going to find that it has high end mil spec matrix security, a bevy of security guards loaded with beta and delta ware and armed with military grade weapons, multiple high force wards, and multiple on site security mages and spirits. The player characters might dominate the accounting firm run and not be challenged, and well that is just fine. They have chosen to run below their potential level and thus get's a smaller reward for less risky work.
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I agree that the relative power of the opposition between given types of facility should scale somewhat consistently, but the noob team shouldn't be hitting zero zones and the prime team shouldn't be hitting single A low-sec facilities/objectives, not from just a dice pool mechanics perspective but from an RP perspective as well. The Johnson that hires a team on their first run to hit a AAA zero zone either gets incredibly lucky or gets what he deserves (as does the new team that takes the job).
The GM does not get to decide what, when, or where the PC's hit. He can have NPC's in the world offer jobs or plot hooks, he can even position those NPC's so that IC they come across strong inducements to get the PC's to do what they want, but he does not have the ability to force it. The PC's can always say "Fuck it." and decide to go knock over a grocery story to cover their food needs for the month.
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In my type of game, 400BP characters aren't already masters of the universe. Sounds like in your type of game they are. Not sure how productive it is to argue about preferences or opinions at this point.
I never once said that 400 BP made a runner a master of the universe, it doesn't. What it does is make him an exceptionally above average individual with multiple complete skill sets at levels comparable to those of individuals who have dedicated decades of their lives to that single profession. If the PC has a skill at 5 then he is one of the best in the world, if he has a 6 then he is an Olympic medal contender or a Blue Angels Pilot or a marksman on the Secret Service's sniper competition team, if he has a 7 then he is Michael Phelps, Fastjack, Michael Jordan, etc.
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So runs aren't supposed to challenge the players? Aren't the players challenging the GM by trying to min-max their characters and squeeze every last bit of munchkin power out of their build to hit 25DP straight out of character creation and/or make every single countermeasure he has planned meaningless? There's no right answer here IMO, it all comes down to how the GM and the players like to play the game.
Whether a run challenges the players or not is up to the players. They choose what they will run against and how they will approach the run. If PC's with the skills and abilities to run against an Ares top secret R&D base decide to run against a Wal-Mart shipping hub, well then they shouldn't face anything that could be classified as "challenging" but the payoff from that run would be far smaller. If the players want to accomplish anything meaningful and do the kind of runs that make their characters legends then they will be running against facilities that are incredibly challenging and with absolutely no guarantees that they won't be sniped by an anti-shipping laser on a blimp 20 kilometers away from the run site, if they want to run a few days a year to cover the rent money by knocking over jewelery stores well; that's their choice but for the characters it means that they are never going to make the massive leaps in power and skill that runners that test themselves constantly can manage and for the players it means that the game could get quite boring fairly rapidly.
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The GM runs the world, what the players do in that world is up to them. Now, the players and GM should talk about what areas of the world the PC's will focus on so that the GM can direct his limited time and resources to more fully and completely fleshing out those bits but the GM has no right to say "You can't run against Wal-Mart, you have to run against Ares R&D because you are too skilled and the Wal-Mart run would be too easy for you.".
If you have played Morrowind it's like that, the PC can run into areas where he will die instantly because he wasn't skilled and capable enough yet, similarly he can hang out in starting areas when powerful enough to solo armies and that is his choice.