Sounds like a fair enough idea, and can't wait for the individuals to have lives and age, that'll be awesome, and races too will be pretty epic. Maybe certain races have different qualities that affect the empire, dynasties, individuals, ships, etc. That'd make this game REALLY deep.
And yeah the epic empire vs living people conflict is real. I reckon for now the best solution would be having options to change time from a few seconds for a year, to millennia per minute or so, similar to what it is now. The latter option would have people being born, living, getting jobs, and dying VERY fast, but unless that takes too much computing power (doubt it would), I reckon it could work.