I recently came up with a way to allow players to sacrifice conventional warfare in exchange for one very powerful city:
The short answer is a single building that is available early on that will give the player an invincible defense, for one city, until very late in the game. On a small map I would think the game would be more balanced if taking capitals was more difficult. I mean after you have two capitals you can usually stomp other Sovereigns on a small map (based on what I know from EWoM and other games like it). You would be giving up hopes of having a professional military, but as long as your Sovereign stays inside, you stay in the game and can focus on magic and questing.
I loved setting up a defense around the capitals in Disciples. Once every few turns the enemy would cast a spell and make a breakout attempt. I would have to quell their attacks, which prevented me from steamrolling over the other players. By the endgame I could send high level units with potions and enchantments over to crush them once and for all, but they were often able to regain power a few times throughout the game. That is how I want to shape occupation in FE.
Of course there are plenty of other ways to build a strategy, but this adds important choices to the game.
There should be a tech called Exit Strategy so we can send it to Congress.
P.S. Napoleon successfully conquered Moscow, though it was abandoned and ablaze when he got there.