This is a huge thing to get right from the get go, and I'm happy to see the topic surface.
We had to deal a lot with this particular problem too, and we have also decided on a shot-by-shot basis. Though some of the advantages worth noting with some consideration for a "master set". If you're doing syflex, and there's a buncha characters walking from point A to point B, the FX side of me would like to have that done altogether. We could run one sim, and the cameras would switch in the set and no preroll except the first one would be needed. Otherwise, you'd have to line up shots back to back and see sorta anticipate syflex in motion and that's a total PITA. You can sorta sim/model your initial state and begin the syflex sim from there, but it's not foolproof. And on the lighting side, one light rig would work and be continous throughout. For some sequences this might be a better approach if the data size is predictably manageable.
Data-wise, master scene don't work well, and that's what ultimately led us to do it shot-by-shot. We are heavy in mocap, and dealing with that much data in one large chunk is just not possible for a studio our size. Sometimes, it's just easier to get scenes to open and work, solving continuity issues later. I personally don't like to wait 40 minutes for a scene to load only to tweak one keyframe or nudge a light for one shot. My only concern is that you mentioned fudging some shots to get composition. This is only my second show, but I'm guessing all layout guys must go to a school where they teach them nothing about shadows, and insist on placing characters and object floating everywhere. Pop in a light and turn on shadows and it looks like a genie went on a rampage in your scene.
It's late and I'm basically repeating what all the other guys have said. But in short, I'd favor the shot-by-shot since it's easier to fix and you'd compartmentalize damages should a file get corrupted. Let the smartie FX guys figure out how to do sims, cause it's not like there aren't tools to facilitate the need. This topic should be taught in CG 101 to both artists and supervisors because majority of the problems that occur throughout a show begins right here, and cascades until it ends up in the form of a train wreck when it hits lighting.
peace,
Lu
