Yeah I generally feel that the game would have actually benefited more if they had just not had the story. If they had just focused on minimalistic "told story" and letting the main narrative be more influenced by and focused on enhancing the "Nemesis" system further allowing for "player stories". The Nemesis stuff is clearly the meat of what makes this game good. Without it the game is sub par, average at best, gameplay. Funny too, because before my brother and I had heard of this game we already had talked about if a game had a system like this.
We sort of envisioned factions that were against each other though. You picked your faction carefully akin to Gothic and Risen and would help boost the ranks of yourself or manipulate events to boost the ranks of fellow comrades. You could be a part of multiple factions, although you would have to be extremely careful to not let other factions know that you are working with another faction or they would try to behead you for treason. So the manipulative role (of exploiting entire wars and events between two factions under your control) would be awesome but would require more care and effort by the player so they don't get figured out. Also we talked about the game world's wars and other various conflicts of interest between and within factions happening without the players interaction, like how this Nemesis system worked. Except in our talks time passed irregardless of whether you made it pass. So events would actually occur whether you wanted them to or not. The basic theme of the game is showing the player that you can't control everything. But interesting enough, in the player's head they want to. So they are going to likely go to great lengths to gain prestige in each camp or in a preferred camp if that's their choosing.
They could have a wife/husband (or two?) and children. You could partially raise your child to uphold certain values that will shape how they grow up. And at the beginning of the game you start as pretty much a nobody. You can choose an easy life and work lowly and/or you could pick a faction and work your way up the ranks. And obviously as I said before you can become a manipulator of factions and work for more than one faction. Possibly even steming a sort of peace between them. Essentially the game won't have an ending. The game would work like skirmishes that go until the player either quits or all the major civilizations make themselves collapse. That kind of game is years and years away though likely.