The Walls have Ears... and Eyes!

This enhanced level of difficulty should be worked into some missions: The Clockworks (or Crey, or some other technology-savy villain group) has taken over office building X. They've also tapped into the building's security system and are watching the heroes' every move on the many security cameras set about the building. They know where you are... They know where to send reinforcements. Basically, the building's security cameras become targetable and act as ambush-spawning devices until they're disabled (working much like the "protect the artifact" missions). Once heroes come within visual range of a camera, unless they destroy it quickly, villain ambushes will spawn at regular intervals. When they're disabled, no more ambushes.
Yes, this makes many of the current building layouts trickier to navigate. The spawn-timer should be set at a delay that's adaquate for the heroes to avoid ambushes if they destroy the cameras soon after getting within visual range. It also makes invisible team members more valuable and forces attack planning in some areas. Make the players think just a little? Not necessarily a bad thing.