I was a bit too focused on the plot and I've thought long about it. I think it would be best if there is less continuity. What I mean is for the players to experience the story at select parts. Give them bits and pieces of the universe and ultimately allow them to fill in the blanks themselves. After all, that's what a game is isn't it. It's an interactive experience.
This method also insisted upon long stretches of time without gameplay and I didn't like that. So there won't necessarily be chapters or plot arcs, rather there will be events that might reveal new secrets about characters and their past and the importance of different environments you explore.