Hellbore, are you talking about the XR-E? The XR-E uses a solid glass lens with a very soft gel inside. I seen from other posts and my own findings. I don't know about any of the other Cree parts, though.
I like the fact that was stated earlier. It is designed to be reflow soldered. It also gives you some added protection when you are soldering near the LED and you bump your soldering iron against the gummy dome of the K2 and SSC P4. It has saved the clarity on many of my LEDs so far. I have massed up the beams of some older Luxeons when I accidentally touched the iron against the dome.
They also add some flexibility to the LED so some force on the dome does not totally mess up the LED bond wires and phosphor or cause the beam to be permanently distorted (like the Cree XR-E and some Luxeons, as we have found). I tried hammering a dud K2 with some pliers in an earlier experiment, and I didn't see any damage whatsoever. As you put some more force (and possibly frustration out) on the dome, it will mess it up though. Never tried it on a live one yet.
I have also heard that it helps dissipate heat a bit better than the acrylic domes. Just think, when you touch a K2 or P4 what is on at full power, you can feel the heat. That heat, although I agree isn't much, could be trapped in the LED dome like the older LEDs. I know the slug is designed to dissipate the heat, but the dome helps some. Any extra heat dissipation couldn't hurt, right?
I like it, but that is my opinion.
-Tony