I did manage to get all the upgrades and win. I had thought the thing with the timers may have ended up being something like that, and I understand your point about the remote controls.
At first I thought the same thing about the client bots, where the frustration of them getting in the way was the point, but after a while it became super tedious and annoying to the extent that it started detracting from the fun. It started making me hope the game would end sooner so I wouldn't have to deal with it anymore. Could just be me, but that's how I felt in the moment.
Maybe making the remote control room-level could work, so you can just click the room and kick off maintenance. That way there's progression to it, without getting rid of the early problem to work around. I could see BufferBot trying to find a way to solve the cluttered client problem.
Overall, I liked the game, and hope to see what other games you come up with.