I realize AI can get buggy in sieges and stuff. I would assume anyone who used an AI army would substitute for real players once it came to sieges.
Another counter to this, and more pro-little guys gameplay would be to add smaller fiefs. For example bandit camps or caves. Just anything that would give more of a battle feel when sieged, and would benefit smaller clans or individual players more to obtain than they would larger clans.
You wouldn't see Swadia or any of the native Kingdoms try capturing bandit camps and such. In native the big guys played ball with the other big guys and for the most part they left everyone else alone, or used them as pawns when they could. This allowed smaller factions to form knightly orders or heretic bands and other interesting groups. It is fun in native to simply have 10-20 knights and hunt down bandits or aid a kingdom. (By aid, I do not mean kiss the kingdoms ass or get wiped off the map as might be more common in strategus).
If we added the chance of prisoners when defeating other groups, you would see a lot more bandits and manhunters. Full kingdom sized clans wouldn't equip themselves all in blunt weapons, it nerfs them pretty badly so they wouldn't be as practical and efficient manhunters/slave drivers as smaller clans who would dedicate to such a task. I could be wrong.
Another thing I feel would increase fun for all players is that you are only allowed to join a battle you are near. Before you count this off immediately, hear me out. When you do join a battle the only gear you can use is your own. With the exception that if you joined your faction's side in battle, you would be able to share inventories. This would allow clans to do what they always do, and would allow roleplayers or smaller clans (with themes of their own) to join the battle as if they came to support rather than joined as common troops. Mercenaries would then have a purpose and be able to make their own influences. If a small clan of heavily armed mounted knights joined a side in a battle, you would see just that. If supporters could use their own gear, they could actually be paid as mercenaries and they could be way more effective as they would be using the gear they are use to. Armies wouldn't need to supply every type of weapon to make sure all mercs can fight, they would need only to hire mercs and worry about their own supplies that their faction will be using.
Anyways I'll stop the wall of text here. One day I hope strategus could be full of immersion and roleplaying and fun for everyone lol.