The problem I have with the set-piece-and-cut-scene approach is that scripted events enforce story by limiting variability. Certain things always happen in new school adventures: at the very least, the villain will antagonize the PCs. You can't have a good reaction roll derail the plot.
I've talked before about listing goals and preferences for villains and how they react to types of behavior, letting a villain's actions emerge naturally from interaction with the PCs. The important part to remember is to not write down what the villain does in advance, but write what the villain would like to do, and when, if appropriate. The part you improvise is what the villain actually does. and the best way to improvise is to inject a random element:
- Use reaction rolls. Not only does rolling a villain's reaction to the PCs make for a more interesting and adaptable story, but it can be used for any undefined situation. The villain's underground lair floods as a side-effect of PC actions in the upper levels? Roll a reaction, if the villain's reaction isn't obvious. What if the villain doesn't care and ignores the flood? What if the villain actually sees the flood as an unexpected boon? On an extreme reaction, positive or negative, the villain comes upstairs to investigate, or sends an emissary.
- Use other improv rolls. For example, roll 2d6 or 3d6 weekly or daily using charts similar to the one I described here to determine the villain's basic behavior for that time period. This helps keep the villain surprising.
- Use wandering monster rolls or event rolls. What's good for the PCs is good for the villain, right? Have a 1 in 6 chance each week that some creature from an appropriate wandering monster chart comes into contact with the villain. What happens? Do they become enemies? Allies?
- Use 1 in 6 rolls in other cases. When you roll wandering monsters for the PCs, give a 1 in 6 chance that the monster is connected to the villain in some way. If you're not sure how... make a reaction roll for the villain. Likewise, if the PCs seek out a new NPC, make a 1 in 6 roll to see if that NPC has a connection to the villain. Just created a special encounter or trick for a dungeon (not the villain's?) 1 in 6 chance it's relevant to the villain's current interests, somehow.