My proposal:
Each guild, once you become the guild master, opens a new guild house. For example, once you become the head of the Thieve's Guild they would open a new front busines (a tavern or pawnbroker or whatever) and you would have an office there. This is where you would give orders to your subordinates and what have you.
If there are functional equivalents to the Great Houses from Morrowind then I would like to see, in place of what I describe above, a system like the one from Morrowind but with greater complexity (and that system shouldn't leave you looking like a middling faction member in a tiny house compared to all of the councilors that you lead).