So I've been thinking on how you can limit the ability of the larger clans without just gimping the game totally.
You have "classes" within the factions. You can allow any one person to as play many roles as the faction leader sees fit(ie, Crazyi The Merchant, Crazyi the Crafter, Crazyi the Scout etc etc). The smaller clans are going to have to put in more time on the strat map, BUT they can achieve what a larger organization can. The larger clans will can have 1 role per person, and thus have to focus less on the map part but needing more organization. Possibly even link the size of the organization to how many "classes" each person may play. Large ones can only have 1 role per person, smaller can play each per person.
Merchant - 1-5 per faction(or whatever you see fit). These guys control buying, selling, and all aspects of trade. There would be a raw resource mini game that connects to the crafters, where the merchants need to keep the things in stock demanded by the crafters. Need iron for weapons, wood for bows and arrows, wool for cloth, etc. How that is achieved I will leave to developers. My suggestion is to segment the map, make each area with a larger city or castle have X villages(X = total amount of the types of resources), each village you purchase one type of raw material from. The gold the merchants have to spend is a flat rate for each faction. This flat rate represents a sort of upkeep cost, larger clans have more members contributing but have to spend more on upkeep. Smaller clans have less they have to blow their money on, but have fewer members contributing.
Crafter - Unlimited BUT your resources for crafting are limited based on what the merchants can purchase, putting cap on what can be produced each day/week and still allowing a wide range of goods to be produced. Who crafts what, and what resources are needed will require communication between the faction. Smaller groups will have an easier time organizing, and the larger ones to maintain correct functionality are going to have to stay very focused(thus making it slightly harder to maintain and outfit a large organization, as it should be).
Scout - Have unlimited(or a limit if needed) - This is plain and simple, a scouting unit. It is fast, mobile unit that may only be caught in combat if it stops. Larger organizations can have more scouts due to their size, thus giving them a slight advantage in this category. They can plot their path much better being able to scout more. A small organization doesn't need to be moving all over the map anyways, they are going to have to focus their efforts in a smaller area. They may also be considered "raiders" and are allowed to pillage unguarded merchants, but can only take a small portion of what the merchant is carrying. That way you can mess with unprotected trade lines, but it wont totally destroy ones economy. More or less a penalty for not having a general attached with the merchant.
Generals - Have unlimited(or a cap if needed) - These are the recruiters and hold the soldier bodies of the armies. They need to be assigned to protecting territory, guarding merchants when they are traveling, and to recruit troops. They obviously also lay siege and engage in battles. You should be able to recruit anywhere. As one travels with a merchant, in each village they roll a dice at recruiting and see how many they get. You can also just set this at a cap per week for each faction, to make sure they do not get far more troops than a smaller clan can. In reality you can only recruit so many soldiers before the population would go to crap in an area and not be sustainable, so I feel the cap is needed. Another way to limit it, is have the size of the strat army effect the gold available to spend on resources. So you can have a small army and pump out resources, and once you have the supplies needed for war begin to ramp up recruitment. It would require a balance between output and solider capacity. You could "relieve" soldiers at any point and time, allowing you to ramp up production of goods. However if attacked in this "production" period you would be in a bad position, and thus needing the ability of your scouts that much more.
**added** Like others have suggested, there needs to be an NA and an EU rating when signing up for battles. When you sign up for an NA fight, the leadership gets to give you +1 or -1. Same for signing up on EU. You go negative and you are going to have a hard time joining future fights, so it is in your best interest to show up, finish, and not be a troll.
Please, discuss.
