I don't think that you got my point about AI management.
Currently, when I play the beta, I usually got 5-6 cities around turn 100, 6 cities means 15 caravans one between each city, having even 3 groups hunting them down manually can be annoying but not that hard..... but lets take a look at a mid-game situation on one of the 64-bit version of the game (with humongous map) and your opponent got 46 cities meaning 1035 caravans on a much greater part of the map, even having 10 groups running around and hunting caravans (or attacking unguarded resource points, etc etc etc) can grow old really quickly, I would rather have a smart AI that I can set priorities to and watch him excequt them alone.
Spying System
As for the Target leadership, I think that this belong to some sort of spying system (a subset of the diplomacy screen perhaps?), maybe we should be able to design and build spies that usually will not be actually represented on the map as a figurine but would act the same way spies acts in total war and EU, they could have missions like:
1. Gather information on tech.
2. Gather information on trade.
3. Gather information on heroes.
4. Gather information on spells.
5. Sabotage technology research.
6. Sabotage spell research.
7. Sabotage production.
8. Sabotage training schedules (make training new troops longer or not yielding XP....)
9. Sabotage food production.
etc etc...
Using spies should not relay on 1 spy per mission but should relay on spy rings, each mission success rate will depend on the number of spies in the same ring in different cities.
For example: lets say that you want to learn what techs your enemy got, so you design and build 1 spy give him the "Gather information on tech" mission and send him to your enemy city that produce the highest research points lets say 100 per turn, the success chance for this mission will be (0.1*RPinCity)% for gaining knowledge 10% in our situation and (0.02*RPinCity)% for stealing or 2% in our case, several turns later you train another spy, add him to the first spy "ring" and send him to the same city but because you already got a spy in there the second spy will only get (0.075*RPinCity)%, or 7.5% in our example for a total of 17.5%, because this city already got a spy in it, but if you send him to the second largest RP producing city with 84 RP than he will add 8.4% for a total of 18.4%. If you add a third spy in the same city the spying coefficient will drop to 0.05
This numbers of course could change from research, spells, spies level, counterespionage etc etc etc...
Designing and building Spies
Spies should be designed and built like any other unit in the game, with different loads for different missions, The spies gear and experience (level) should determined their Spying coefficient their "Don't catch me" coefficient and their counter espionage coefficient.
Example: Lets say that we want to build an info gatherer guy, so we equip him with fine cloths (i.e merchant disguise) to raise his "Don't catch me level" and we equip him with "Bag of bribes" (raising spying coefficient) and a potion of disguise (very expensive big boost to both spying and "Don't catch me " coefficients).
Spies training times should always be much longer than normal soldiers training time.
Spies are only trainable in the palace or special espionage schools that comes later in the espionage tree (barracks like building only for spies).
Army Logistics
I agree in general about the armies supply lines, each soldier should have an upkeep the most basic one and generally unchanged one should be food, each soldier should count as 1 citizen when it comes to total food consumption, beside food, each soldier should cost an upkeep of a percentage of the materials that made him.
For example, if a lightly armored archer cost me in materials 0.5 leather, 1 wood, 0.1 iron than the upkeep of said archer should be something like 0.1 leather, 0.2 wood, 0.02 iron....
Upkeep costs should varies according to what the army is doing, an army in garrison duty should cost less upkeep than an army that is actually fighting.
I think that when an army is on the move it's supply should be represented by caravans, those caravans could be attacked and defended just like in any harassment mission, the longer an army does not receive supplies it's attack and defence modifiers should drop.
And to finish, here is a cool spell for eviiiiiiil players.
Consume essance
Basicly, you take one hero/wizard/channaler that got essance kill him and absorve some of it's essance, this will inqure a large hit to prestige, foreign relations and hero recruiting chances.
Warder