A bit of a radical idea but I'm thinking, what if you the player cannot control how the fort develops / what happens / what the dwarfs do fully, you have some effect on development of the fort but it also kind of develops on its own partly independently.So in this case you or I the player is actually a dwarf from the first expedition. Expedition leader maybe. There is a sort of fog of war (like in the RTS games) so you only see within your line of sight (or information other dwarfs report to you). You have to give commands and plans to the dwarfs and they carry out tasks, you can visit sites and give direct commands or give dwarfs general instructions. (there could also be a progression from peasant up to king with more dorfs reporting to you)
but dorfs also may make (?minor/major?) independent decisions. The difference here is the full power you have over what happens in fort is replaced with less-absolute power. You do not at first glance have knowledge of everything going on in fort, This could add to much confusion, tension and trouble at times of crises. (If there is an option enabled for switching characters at will you might switch to a military commander character in a siege)
and the dorfs may or may not do what you tell them. Here they may take part of the instruction from another authority (noble?) / or another collective. Eg. If a King or Queen resides in fort and you are not playing as this character, you may have less authority and say on what happens, I imagine there could be a mechanic where dorfs revolt or mutiny which could be much "fun".
I don't think this system needs to be completely rigid (or you have the choice). Perhaps you can switch the character you see the fort through as you like (or in a more restricted way depending on options chosen). Possibly you could summon any dwarf you like to report, or you get a static view of fort periodically.
One problem I see is how good dorf AI has to be for independent work and plans. What do you think.