My 2-3 biggest suggestions are:
Bot AI:
Tactical, aware of their surrounding, a more agent-like system with personal needs balanced against an overall directive depending on the tribe/commander (organized Spartans, cowardly thiefs etc...). I'm aware that this is one of the most difficult things to implement, but that would be the greatest thing ever.
If you managed to implement it, add immersion by showing the troops desire/state/intension, add communication, troops sometimes screaming commands like "form a line", "incoming cav" (SWITCH WEAPONS), "arrows now!", "shields up", "stand off" (SIEGES)... or just running away crying "ahhh, help, mum" or simply relay and repeat your commands to soldiers far away.
UI overhaul (not before M&B2 i guess):
And by overhaul i mean: Delete the Files and redesign the whole thing from scratch.
I know the menu style interaction is probably very, very Mod-friendly and easy to grasp, but in M&B its definitely "
function over form". Not good, i miss simple things like a button to (easily) browse between my companions. There are at least 30-40 little things in the UI that completely ignore even the very basic "
never ever do this to the user" guidelines and add hundrets of unnecessary clicks.
I lost sooooo much time just to click up and down the stupid menu hierarchy, to a point where i simply ignore the urge to make small adjustments and save it all for a "
terrible 5 minute non stop click orga session once per hour" while preparing fresh coffee anyway.
The whole thing feels like a wedding invitation written and designed in Excel.You get the point.

Some Mods add missing functionality, but just within the limits of the existing UI.
Companion Vassals:
It seems most of the abilities, like surgeon, trainer, path finding, tactics are not taken into account when a companion becomes one of my vassals. When i sacrifice one of my worthy companions, a potential fighting juggernaut of destruction, with 150K equipment and 10 trainer, i expect him to do better than Lord "XY".
Another annoying thing:
"Enemy AI wants you, dead or alive at all cost, cheating allowed!" Its doesnt matter if there are 10 better, tastier almost naked targets without armor 10 meters away from the enemy archers or not. I am 200 meters away on my charger, covered in full plate armor and helmed, yet the very (miili) second i lower my shield, i get 20 precision arrows in my face. Enenmy AI often focuses too much on the player, especially the archers/ranged. Maybe the Loot- or Leadership skill should tune down that attraction a little.