First off, I've been waiting for a mod like this for a looong time, and I'm loving what I'm seeing so far!
Here are some ideas for future versions, they're pretty big but from what little I know about modding in M&B, I think most of them could be implemented at some point in one form or another. I was going to post this in the random ideas thread but then I typed out this massive post, sooo here you go:
1. Interaction among soldiers.
For example, the cook, quartermaster, sergeant-at-arms, bodyguard, etc. Easy way to implement this is to have generic NPCs, harder way would be to have each NPC unique with their own relationship statuses. Then you could implement something like, do enough favors for the quartermaster and he might give you better equipment. In any case, perform tasks for other soldiers in exchange for renown, XP and $$, and maybe get noticed by your lord and improve relations with him.
2. Utilization of non-combat skills.
This one would require some extra brainstorming, one thing I'm thinking is random events that can either have positive or negative effects on your standing (and rank) depending on the outcome.
Examples:
Trainer - Once at a higher rank, a random event can occur where somebody tries to infiltrate your camp. If you have high Trainer skill then the guards will be well-disciplined and will catch him, then you end up getting a reward for enforcing good discipline. If you fail the skill check, the guards will be asleep at their posts and the infiltrator will steal something or nearly assassinate the lord, then you get chewed out and lose a small amount of relation with somebody for your men's lack of discipline (this is how a real army works, "**** rolls down-hill"!).
Spotting - When selecting "Follow your commander into battle", there is a random chance that the enemy will be ambushing your army. If your spotting skill is higher than a random number between 1 and 10, you're able to spot the ambush before it happens, gaining renown/xp/$$/relations.
Pathfinding - Your lord appears to be lost but he won't admit it. You can offer to guide him, if your relations are low and you fail a Persuasion check he'll ignore you but if he's at least over 1 or 2 he'll agree. If you succeed you are rewarded, if you fail then the lord punishes you for making him look even more like a fool.
Tactics - In the same situation as the spotting thing, if your skills is high enough and you pass the skill check, you automatically realize that your army is maneuvering into a poor position. You can then choose to attempt to warn the commander, now there is a small relations/Persuasion check to determine whether he listens to you or not. Either way, you get rewarded for either avoiding the ambush or being able to say "I told you so!".
Tracking - See Spotting/Tactics, except you notice something suspicious about your environment that leads you to attempt to warn your commander.
Looting - Find bonus items after battle, or maybe just $$.
Engineering - Build a "Trojan Horse" during a siege, or maybe discovering a structural weakness allowing you to infiltrate the castle/city, allowing you and a small number of soldiers to skip the main siege battle and head straight to the streets/keep. If you succeed in killing everyone there, you get kicked back out to the main siege battle but gain a large reward for "wrecking havoc on the enemy". If possible, battle advantage gets increased drastically to simulate the enemy being distracted.
Persuasion - Can be used for resolving disputes between soldiers, improving your reputations with them or gaining other rewards. Also for convincing people to rebel against the lord, or convincing the lord to do something (like in above scenarios).
Leadership - Can be used as a requirement for idea #3, or maybe for inspiring soldiers before a battle.
First Aid, Wound Treatment, Surgery - Your army captures an enemy scout, but after attempting to escape he took a spear to the gut. Save his life and then use your Persuasion skill to get information out of him, or Trade to bribe him with the idea of his potential freedom, or Ironflesh to intimidate him. If he dies, your Looting skill might allow you to find a hidden map on him, but your reward won't be as great.
3. Become a sub-commander.
In addition to gaining normal promotions, have the option of being promoted to Sergeant or Captain after fulfilling certain requirements (leadership skill, # enemies killed, renown, etc.). Then, once in battle you will have command of your own small number of troops, or maybe something like leading all of the cavalry units in a battle.
4. Renown-based promotions.
Gain renown for fulfilling certain achievements. Your starting rank will take your existing renown into account, but not too much, and after that it will just depend on renown you have gained since enlistment. The first couple of promotions require small amounts of renown, but after that you need to become "famous" for your actions in order to get recognized, finally having the option to become a lord after a certain amount.
This way a guy with 100 renown before joining an army won't start as a recruit, but won't start as a knight either. If you have over 150 renown (thus could just become a lord yourself if you felt like it) then the lord will still enlist you but will say something like "I've heard of you. Remember, you work for me, don't get any funny ideas."
If at any time you have negative relations with the lord, however, then no amount of renown will allow you to get promoted.
5. Random events based off of commander's personality.
I think someone else in the random ideas thread had an idea like this. For example, if your commander is "malicious" then he rewards cruel actions. There could also be random events where he is mercilessly flogging some soldiers for basically no reason, if you stand up for them then you have a better chance of leading a revolt, gaining renown but losing relations with the lord. Plenty of opportunities in events like these for using non-combat skill checks, too!