A wargame I own has a system like this:
Commanders have a leadership radius and troops in that radius get a bonus dependent on how good the leader is and dependent on how far the troops were from the leader. The radius is the same for all commanders to make it easier on the players to know what is going on, but better leaders give better bonuses. Leaders would have to have to have a certain "Leadership Rating" to command the troops in its radius. Each unit would have a leadership cost, thus you could simulate elite units being easier to command and peasants consuming a disproportional amount of command points. If a Leader didn't have enough command points, the troops in its command radius didn't receive any bonuses.
Supply is a fixed number of "spaces" from a city but can be extended by a Unit with a Leader. For exampler, you might get 150 supply points. Everything withing 150 points of a friendly city get supply (supply can be blocked by enemy units. To determine supply, each terrain type has a supply cost. Roads cost 1, mountains cost 30, forests cost 20, etc.. As long as a leadership unit is in supply, he counts as a source of supply with another 150 points. So if I have a city in the mountains with no roads, it could supply 5 spaces. If I had a commander on the fourth space, I would be able to get supply 5 additional spaces for a total of 4+5=9.
Each unit also has a supply consumption rate and a supply reserve. Once a unit is cut off from supply, it starts using its reserve. Once the reserves are gone, it is severly handicapped. This system is slightly abstracted but creates a ton of tactical challenges. I found this system flexible enough to simulate WW2 east front, but simple enough that supply didn't become too big of burden. There was a supply overlay so you can see what spaces were in supply by each city, or overall supply.
Skill of the troops was reflected by the units statistics.
With this system, the game had the following pros and cons:
+ The ability to model any type of troop. For example: Elites units could be represented with High cost, high power, low supply consumption, easy to lead and peasants could be represented with low cost, high supply consumption, low power, hard to lead.
+ Leadership made a big difference
+ Supply mattered by wasn't overly complicated
- Supply and leadership systems make the game more complicated and could act as a barrier to entry. there would need to be some good tutorials and in game tools to make the system easier to understand.