The main feature I've added here is electrical systems, and initially doors controlled by them. The generator in the upper bunker is powering the door in the lower bunker. When the spreading goo interrupts the power cable, the door loses power and opens automatically. One could imagine a number of aggravating puzzles based on the principle of waiting for spreading goo to accomplish some action before you can proceed -- but don't wait too long! Or, even deliberately introducing goo into an area in order to progress.
The other minor feature is a change to the goo spreading rules. It used to be that walls would only fall if they were exposed to goo from both sides; now, if one side of a wall is completely covered in goo the wall will succumb after a few seconds. I like this effect better, since everything about this game should be designed to increase the player's paranoia.
This particular recording was done using QuickTime X to record the entire screen and then MPEG StreamClip to crop it, but the process was still a giant chore and the quality isn't much better. It's looking like I am just going to have to (gasp) pay for some software already to take care of this.