First,I'm still of the mind that a captured wagon is best used for your own purposes and kept on the map.
Secondly the wagon system could be eliminated all together and replaced with a virtual supply system that could be determined by the chain of command or location on the map of units to supply depots. Or by other means. I like the wagons.
Thirdly, You could capture a wagon get the points for it, then diband it afterwards, if it's going to be a pain in the ass. (Need dsband button)
Fourth, After resuppling all my troops,guns and whatever just before a carry over scenerio ends, (killing the clock let's say), only to find these same units low on supplies the next scenerio bums me out, which at time I want to blowup the wagons.

Fifth, If you are capturing/killing wagons you pretty much have a handle on the battle anyway. More so against the AI.
Sixth, Yes, I agree that adding demensions to the wagon/other aspects of the game would be more entertaining, there's no doubt about it.
At your service, Hoistingman4