They were always there. I always thought it was something to do with the colour they superimposed over the emperor's eyes to give them that glow overlapping onto the cloak hood. As for improving the make-up for ROTS - bullshit. The make-up in ROTS is terrible. Looks like a rubber mask you buy in Toys 'R' Us. But let's not get into that. Didn't they try and work them into the continuity buy saying they were parasitic slugs that fed on the dark side energy and lived on the Emperor's face? Or was that just a joke? It's hard to tell these days, I'm not sure if stuff like that is meant to be a joke or not anymore. I'm surprised they haven't treid to say the garbage Mattes on the TIEs are deflector shields (which is actually pretty feasible)