I'm very annoyed when the game lags server side, my computer run smoothly and my connection is fast(100Mb). But when the bot movements is laggy and sometimes "teleports" my only guess is that the server running the game is overloaded. Especially when a player from another team can cause my bots to lag. And since the game is lost if the commander dies it got me thinking that it's because all commanding/CPU power lies within. Why not make it a part of the game economics. Just as with power and iron you have a CPU bar. You could build command relays that would increase the available CPU, perhaps even some mobile ones. If you put vehicles on patrol or with any actions they will consume CPU and when all is being used, the remaining bots will be unusable until you either build more command relays or stop the movements of other bots. Another way to look at it would to have a limited number of CPU resources per player, that way you could be sure that your army would run smooth and if another player choose to build too many bots it will only penalize them.
But there already is a limit as I wrote(disregarding those players that like the lag). So in response to your reply, yes it is a good idea.
The game should have limits in the lobby menu. Besides that, the game shouldn't because its entire key is macro scale. Besides, computers will only get better. Right now, the game is unoptimized, not cleaned up the code to run faster, unit masses aren't instanced but rendered one at a time. The servers, they are Amazon servers, and run 8 games per server. Really, these are the things that weigh things down. So, this request is way to unfounded yet. You aren't saying the game runs slow late-game. You are saying the testing runs slow late game.
I can just imagine a 0.1 eco rate with the CPU system. "Sir, we require more pentiums to process your request for movement!" It's silly and there are better ways to improve server-side performance.