But despite them, these major empires are upheld. Realms like Ibladesh and Sirion are just too large (in a fun to play aspect).
But maybe the penalties is not where the problem lies. Maybe something else that encourages more secessions. Like somehow giving the secessions increased likelihood of surviving.
Player culture. They already have enough incentive to break off, but chose not to. There's a limit to how far we should go to force people to act as we think they should. If they don't want to break away, no amount of penalties will change this.
