My preference would be for them to jump any such story ahead at least a century or two, well after Shepard is dust. That way you have a nice blank slate on which to build a new saga. That way you don't need to come up with some conceit as to why Shepard is no longer involved in larger events.
One of the main things that bugged me about Dragon Age II is how it basically brushed off your DA:O character with some offhand remark about how The Warden had mysteriously disappeared. My warden didn't (nor could she) go through the mirror at the end of Witch Hunt and as far as I was concerned she'd retired back to Highever with Leliana. I imagine it was even more irksome for players that actually killed Leliana!
So yeah, I think giving the story some distance would be the best way to continue the story without disrespecting players' individual experiences.