I too am contemplating doing this. The solution I have chosen is:
Each character makes a shadowrun character with around 500 starting points (plus a big wodge of points for the following). They are all immortal elfs. Either princes of one of the Tir's or an independant. The present day game is mostly a political game: council meetings, house politics, vendattas... but very little need for personal power, as these characters have people to do things for them
A deadly threat is coming close (horrors are good: I like Harlequins back), and they need to find out about it. In order to do this they need to "hero quest" into the past. This means that they relive the memories of an event in the past. But due to powerful immortal elven magics the past is effectively real. They are the same powerlevel that they were in the past. The past now can be in several places and times, as they chase the clues: before the kaers closed. During the time of horrors, Earthdawn, world war II...
Each place in the past will have a theme. They get points to keep from their character (so each time period they get to loose a different number of bps). Consistancy is not ultimately important, as this is an astral quest after all, not actually the past.
So this is a bit like a time travel game, except that all they are doing is reliving the past. They are actually there though, so they can die.
This type of game works best if you have a clear story with a beginning a middle and an end. It might be fun to start on an astral quest, then when they wake up, they realise who they are.
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Providing cross-over events is trickier though. They'd ordinarily be tricky anyway, because we're talking events a good 10,000 years away from each other. By pulling them into the same timeline you can rationalize "why didn't we know last week" more easily, but have a harder time providing a cause-effect relationship.
Aha we see that this problem doesn't exist with this approach to the crossover game: the characters know they are in the past, but they are legitimately their and interacting with their friends, families and enemies from the time. There are no cause and effect, and the "why didn't we know last week" is because we forgot and are going back into time to remember. (I bet its hard to keep track of memories after 10,000 years)