I've been in scenes that have taken a half an hour, and occasionally more, to set the "pre-scene powers, rolls, and equipment". WoD, you saucy bastard.
2-3 hours per scene is a good solid number. I normally see the scene start to fall apart by then.
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I started answering the questions in the OP then I realized: I'm answering these no differently than I would for people asking how to run a module for a tabletop group. The answer is that there is no single answer, that you read the group and adjust based on that. Knowing how to do this requires experience, and gaining experience requires participation. I don't think a survey is going to cover all the differences in play that we have.
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- What duration - as measured in hours - is ideal, acceptable, tolerable and (if there's such a thing) 'too much'?
"Too much" is when the people involved say they're done. I'm going to stick to my 2-3 hour number for now.
- How easy is it for a PrP runner to predict how long a scene is likely to run in the first place? What are some good ways to make rough estimates?
Run plots. Pay attention to how they worked out. Keep running them.
Be in plots. Pay attention to how they're run. Keep paying attention.
- Should a projected duration be advertised as part of plots?
Duration in hours, or in number of scenes? Is this even possible? See Above.
- What's the proper way to break longer scenes down?
The way that's most natural for the scene and those involved, though I would argue "one scene" is always completely over when the scene itself is over. If it's going on too long, then learn from it and don't do that again.
- How do you handle players having to go in mid-scene due to RL
The same way you do any other scene: Either there is an out for them right there, or you work out the consequences later.
It would be completely dickish to force a negative consequence because they have a life. Remember Rule #1: RL Comes First. If there is a negative consequence, make it interesting or at the very least make it because they were on the losing side.
All IC situations come from OOC considerations, from the very plot to the decisions people make to stay in or get out of it.