Right now I'm kinda leaning toward the "Generals and Commanders" mod that Grey Fox was working on. Having the "Great Commander" be a unit that takes to the battle field, provides benefits of more than just "free xp" and can be targeted by the enemy (who better to attack with assassins?).
Upon creation, you could select a "trait promotion" for the unit (Siege Expert, Fearless, Tyrant, Caring Commander, Master Archer, Zealot etc), each of which causes units in his stack to AutoAcquire relevant promotions.
Certain traits would allow the commander to be "merged" with a bodyguard unit (traits that basically allow the commander to take to the field and fight himself) - doing it as a unit-merge allows you to assign your best unit of the era to defend the commander so that his strength is appropriate.
Other traits would be less directly combat related, but may have additional levels to gain as the unit levels up (a Siege Expert may grant City Raider I initially, but later allows the construction of Battering Rams or even Trebuchets, a caring commander would boost heal rates initially, but later may be able to use a spell similar to "Heal").
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There are a lot of different options that don't rely on existing mechanics - this is just one. I don't think having a great commander as another type of specialist is the most interesting way to do it. Very easy to implement that way - but I think there are probably better things we can come up with.
Ideally, I'd like to use the completed GF version - check
this thread for details. What I mentioned above is just a very simplified version of that (one which I could probably implement in a weekend).