1) Better skill/stat system and skill stacking.
Most of the skills are fairly useless in M&B. Looting and trade are jokes and the Chrisma stat is only useful for it's own benefits and pumping up leadership.
Skills should stack within your party and with all your soldiers. Meaning if you got a whole bunch of "Banner Bearers" with high Leadership you could field an army with greater moral, the same would go for nurses and the like.
I don't like that almost everything about the army comes back down to you or your companions.
2) Better medical system.
Right now your men either get knocked down and you have to wait a day or so to get them back or they just die. A better medical system that have all units have HP loss (like companions) would allow for improved combat. It would stop you fighting endless battles if you've got a high surgery skill.
3) Improved Tactics and Minimap.
This is the big one. There needs to be a better minimap with the terrian and highmap so you can better plan your troops. It could even have an rts themed map where you could drag units and change their formations in/before battles.
4) More to do apart from combat.
he combat is great, wonderful infact. The only problem is that it does get dull, very dull if you get a strong warband that can steam roll pretty much anything.
More sandbox elements should be added like landownership, better trading, better questing and other things to distract you from combat.
5) Improved cities abd general polish.
RIight now the cities are just dull and boring, with the same copy pasted citizens offering you nothing. They need to be reworked completely. There should be a point to the cities apart from a place to sell crap.
Not having to leave the city for anything interesting to happen at early game would be the aim here.
6) Better troop management.
Troops would need to camp and eat every so often or a moral hit is taken. Options for various "privileges" for your troops to increase either their moral or discipline, things like allowing camp followers or having an "open lootting" policy.
Not only will this add more depth but it allowes on to role play a bit more. You could have a band of merry rogues or an army of heavily disciplined soldiers.
7) Better Army Upgrading.
Pretty simple. Soldiers get more experienced through training or combat. Once a unit hits an experience level instead of being upgraded on the spot he would have to go back to a town or to camp to be upgraded.
Simple Crafting.
It would be nice to have a way to equipt armies outside of towns. Thats where the new crafting skills could come into. One could invest in these skills to gain money or to equip their armies. Blacksmiths or soldiers trained in these skills could be used as well.
9) Better Honour/Reknown system.
Reknown would be almost the same with a twist. You'd get reknown for pretty much everything. Reknown would work as fame and how many people know you, reknown could be gathered by killing bandits or by leading a small army against a big one.
This mixed with a new system called "Glory" (which bascially measured how well you win) would mean you could be famous throughout the lands as that joke that leads his army into massacres.
This would make interacts with cities/lords so much better. Honour would stay largely the same.
10) More Options with fiefs.
A fief should be a very important thing and having one should be more about getting taxes and some new recuits.
The possiblities to do with these fiefs are endless and I'm sure you can all see the potental with running a city or village.
11) Combat.
It needs rebalancing a bit. Right now theres the famous problem of heavy cal. stomping everything.
Larger battles and deadlier weapons should mean that even if you're running a vast army of peasents you shouldn't be stomped over by a couple elite knights. Bigger maps would also alow for more tactics.
Seiges could do with some work. You should be able to devide your army to keep them sieging a fief while you go off and do your thing. Siege weapons should also be added to help crack open the walls instead of having all 389 of your troops trying to cram onto. Some simple form of building defences both for the attackers and defenders should allow for longer seige battles with clear lines that are more evolved then just zerking over the top of the battlements.