ITEM #1: Making the sovereigns distinct from one another
Heroes and Sovereigns have no skill-trees or abilities that can be learned upon leveling up. Right now the leveling system is rather bland. One of the things that made masters of magic so fun for me was the ability to customize and grow my heroes by selecting new abilities for them.
I never played MOM but I totally agree with the fact that the levelling system as it is now is not really exciting. If you want to play a game for months on a gigantic map, as Brad stated somewhere, that system need a serious revamp.
I came up with two ideas that could spice up the game a bit, in addition of the old: new level = new ability approach.
Dynamic traits (talents/weakness):
What I was thinking here was traits that are modified by your actions within the game.
Let's take for example "Cruel" there could be at sovereign creation a slider called karma, that goes from "cruel" +x pts to "kind" -x points. The level of karma could impact the moral of our troops and the likeliness of champion to join us, for example a "kind" sovereign should attract "kind" champion... and the moral of our demonic/dark troops could be lowered.
If we start the game with "Cruel" karma, during the course of the game we can then work our way up/down depending on our actions toward NPCs, helping people during quests...
Some other examples:
Brilliant / stupid (sanity) linked to the tech research bonus (+x)/minus (-x if stationed in city) and be modified depending on some achievements done during the game like build 5 study (+1sanity)...
Tracker / clumsy (logistic) could be linked to beast hunting achievements, or amount of the map explored... and impact movement points
Cowardly / intimidating depending if you have flown many battles or won many battle against all odds,
Dynamic abilities (profession tree):
The idea is simple but is as great potential ; you start as an "initiate" of your profession and then improve to "apprentice", "master", "grand master".
The easiest way may be to unlock a new rank every x levels, maybe after executing a set of quests as well ( for the higher tier ones).
Each mastery grads should withhold a certain set of skills linked with the profession, that could be used independently (like back-stab, set trap, infiltrate, poisons, etc. for assassin)
It really adds depth to the concept of profession I think.