Maybe this was an obvious one, but… yeah, bad-guys have to be prepared.
When GMing with Sorcerer’s Relationship-Map method, you (the GM) don’t decide who the main villain is; that comes out through play. You start with lots of NPCs who each have their own motivations and plans, and who will each try to influence, recruit, help or hinder the PCs accordingly. As the story develops, one (or more) of the NPCs will naturally end up opposing the PCs or trying to harm them.
My problem is: twice now in the current game, an NPC that had the potential to develop into the main villain has ended up dead. In their very first interaction with the PCs.
I’ve been statting up these NPCs as if they were some-what experienced PCs, which I see now was not the right approach. These are ambitious and dangerous people who already have a number of enemies. They should each be walking around with the equivalent of a couple of Glocks, a kevlar vest and six body guards. With a bullet-proof limo idling out front.
The prepared bad-guy was practically built into the dungeon-crawl model of play. A whole maze of mooks, lieutenants and guard-dogs stood between the heroes and the villain. In the new democratic world of R-map play, I will have to be a little smarter. Or at least, my antagonists will have to be.
-J

One way that I have handled this is to remember that as the GM, I cannot reasonably be expected to think of every possible contingency for a villian. Players can focus one one entity (their PC) quite effectively, but the GM ends up having to spread their attention around.
In OD&D, I get around this by making a simple ‘INT’ d20 roll every time the characters come up with a plan. If the die roll is the INT score, the players have caught them unawares, and get the full advantage of surprise.
It’s a quick-and-easy method, and is transparent to the players.
Thanks Sandy, good thought! There’s not necessarily anything unfair in me beefing up an NPC’s preparations (or counter-measures) on the spot. Just because I didn’t see it coming, doesn’t mean the NPC didn’t.
-J