Facebook yesterday to reveal a new behind-the-scenes image from the film and to tell the full story on Lee’s original cameo appearance.
“In the original cut of the film, when the Guardians enter the Collector’s museum, Rocket looks over and sees Cosmo the dog in one display case, Quill looks over into another display case and is surprised by a tentacle slapping against the glass, and Groot looks over and sees, in another display case, Stan Lee. In one take, Stan Lee just slowly turns up his finger, flipping off Groot. We shot this footage with a Stan Lee double because Stan wasn’t able to come to the UK at the time. The plan was to shoot Stan in the same lighting when I was back in LA, and we’d digitally replace the double’s head with Stan’s actual head (not quite as difficult as it sounds). Although I thought the cameo was funny, I thought the flipping off joke was too similar to the moment earlier in the film where Quill flips off the Nova Corps, so I excised that part of it immediately. A couple of the guys at Marvel thought Stan Lee in a case was too broad of a joke in general, and that it took the audience out of the movie. I argued about it for a bit, but we ended up not keeping it in the film.”
And I guess it would have fallen too much into the, "Is Stan Lee, The Watcher" conspiracy.