You imply that managing nobles in a bureaucratic empire is inappropriate, but you can focus gameplay on handling specific important people (as opposed to giving abstract orders to faceless organizations) in any social structure.
On a more serious note, just managing nobles seems meh to me. As King of Men said, if you want to manage nobles go and play CK2, it portrayed it very good. I don't think I woulod be able to do it much better than they. Plus, I lean more towards a bureaucratic empire, like there is this emperor and organizations, guilds, corporations, social struggle, spreaders of dangerous ideas. Less feudal and more modern (not that they can't be nobles there, I don't have anything agains them, but just limiting it to nobles seems not so great to me).
If nobles have a limited importance for the Empire and the Emperor (e.g. as sources of succession by assassination plots, as marriage fodder and as trusted diplomats), the game can bring to the forefront other types of important people: generals and heads of bureaucracies, political or religious leaders, scientists and artists, entrepreneurs and managers, and all other relevant types of powerful or influential special persons (e.g. fairies or alien visitors, artificial intelligences, superheroes of all sorts, wizards...).