One way of micromanaging the entire map and avoid the "living factions" to expand too much or historically wrong and play the game at a slower pace:

Use toggle_fow in the console, check out for the Apisthemenoi (sp?), the vanilla "brigands" which spawn randomly in the map. Move those who spawn in a non-eleutheroi territory with the command "move_character", just outside the rebel towns that border non-rebel territories. The best position to move them is right in front of the route that the invading army will use to reach the city. Check each turn that the stack hasn't wandered and if it did, move it back as many times as necessary. Sometimes when a faction moves an army into that terrory and needs at least 2 or 3 turns to reach the settlement, the stack will enter the city and join the garrison to defend in the upcoming siege. Those 2, 3 or even 8 extra units will make a diference in the autocalc. If the stack did not enter, the defenders might sally out nonetheless because they have reinforcements, and the AI won't sit behind the walls until its starved to death.

If you do this each turn, you might be able to build quite an important defending force for many eleutheroi towns. I prefer moving the stacks to the closest eleutheroi town in relation to the point where they spawned. So you get Celtic Spearmen/Archer/Slinger defending Celtic towns, Numidian Skirmishers in Numidia, and so on. When the game progresses, you might be forced to create some curious stacks (Indian Elephants in Central Europe, Sauromatae Archers in Axum, etc), but it will work. The AI will be forced to send full stacks to take the cities, otherwise they will get defeated or the city will rebel because their troops took such a beating that they have too few soldiers left for a decent garrison.

The only rule I use, is not to move rebel stacks who belong to a rebel "ethnic group", unless their settlement has been captured, and it didn't rebel back. You might notice that some rebel armies have the "Tauri", "Maka", "Cottinii" names in brackets. That means that I try to keep those stacks close to the city they "belong" to, so they defend it when its invaded. If their city has fallen, and didn't rebel back in 10 turns, I move them to the closest eleutheroi town.

One tricky place to do this is Germania and Central Europe. The stacks you moved there might get hidden in the forests and you won't be sure where they are. Also be careful if you moved stacks there and you invade, between the ambushing hidden stacks and the roving defenders, you can make Varus look like Julius Caesar.