I fully agree with Ted, using spies should (in most cases) lead to delaying of edited plans. Troops should start executing original orders and then, after for example two weeks, abandon old instructions and follow edited ones. That would make much more sense. That would also encourage players to use spies in more logical way, to discover the road ahead of their armies (to make edits possibly small and thus delays possibly insignificant) instead of sending them to the other part of the world and editing orders basing on news received from other part of continent. And even if the spy is already on place, then delivering the news, preparing new orders, delivering them to an army, etc. still should take time. You've once tried to explain me your theory about pace of movement of units and teleportation of spies doesn't seem to fit it
I also think that whole idea of Late penalty is missed. It's all nice and fun when the only thing one has to worry about is math homework, but it's getting harder, when at the same time you have to study, work, prepare your thesis, etc. and of course you have to discuss your actions with several player who all have similar real life duties. One of major advantages of turn-based games is their time-independence. Why would we get stripped of it freely? Personally I don't care if I have to wait a week, two, or maybe a month to see an update. It's just a game, and I prefer to know that both my allies and my enemies had time to prepare their orders in peace, to think of best solutions, than to just play as fast as possible aware, that half of actions in each turn makes totally no sense due to lack of time to prepare them.
But I like the overall idea of limiting usage of spies. But maybe not by strict limit (as you've proposed), but rather by lowering change of success depending on number of used spies? So if you use just one spy in a turn, then probably he will succeed and bring a lot of info, but if you send four of them, then almost surely, all of them will fail. Strict limits are boring, they make game predictable.