Actually, now I really want to do this, so let's take a vote. David, try to contact Whizz and get his opinion too, since his chars will eventually be involved and all, plus he's still a huge part of MR. Pinkie too if you can.
The options are:
- Multiple games, one per era. This would allow for more concise paths and overall story following, and would give a new experience for each reoccurring char due to the changes they go through from era to era. This would involve an AU where a new character, the player, is introduced somehow and go from there.
- One game. This would make it infinitely harder on me to design, and the final game would be MASSIVE, likely have inconsistencies, and would have different endings depending on when you romance someone, including furthering the game beyond getting with the char you want where you have to manage to stay with them during the following events. 
- An AU AU where it's all the chars, but basically all as regular beings rather than the way they are in MR. Events and changes in personality would still occur parallel to how they did in MR, but the reasoning would be different. Basically, imagine it as "all the chars are in highschool/college where laws are really loose and fighting and murder are common." Again, this would either need to be in an era by era basis or as a single game.

Personally, I vote era by era, though whether it's in MR proper or in a single world AU doesn't matter to me.