Great Game, I would extend this on many ways, as your GDD mentioned: Upgrade system would fit the game perfectly!
Maybe some Clicker events on BugScanner or a Firewall visualy burn over the screen pushing the bugs back. Bugs biting the programs with healhtbars so you have to defend your Programs. or bugs drop programs you have to delete! Great game, which made me think about extending it alot - I got very into the mind game with this Great submission!