Undoutedly, this is by far, the most interesting feature in the game to me. It's implications for reducing the micromangement hassle of large empires is - just that alone - incredibly appealing. I'd like to get my mind around what are the pros and cons that come along with attaching territories to a regional city/capital.

I would add a income loss on all income of the attached region at the start. To simulate transport efforts that need to be made.  And after researching some tech like the wheel loss is reduced and later with better roads and railways its removed. 

And the loss could be scaled by distance to the city center.