I came up with an idea, allowing the storage of troops in allied cities. Although currently not allowing that kind of thing does add to the challenge of the game, allowing it opens up other doors. Players that have troops in an allied city cannot send a truce nor declare war while they're in a city. To prevent a giant stack (which itself has weaknesses), perhaps limit the number of allied troops that a city can hold either per player or a set maximum regardless of the number of players, so perhaps 50, which is the biggest stack you can place in a city in the scenario maker. When a player leaves the game, the allied player with the largest number of troops in the city/cities gets to keep the city. Note: both players need to be allied to each other if they both have troops in the same city in the first place.
Similar idea, though not as detailed nor covers some problems:
http://atwar-game.com/forum/topic.php?topic_id=9910&board_page=6