Palpatine dimmed the lights so that it'd be harder to see him, allowing him to speed through the room undetected and kill the Jedi. The flicker effect also has a secondary purpose: it hides that terrible CGI-Ian McDiaramad's Face-On-Stunt-Double-Effect quite well. :)
Actually, this BobGarcia guy has some fantastic ideas for drastic changes to ROTS. Here are a few that caught my eye. Most of them are just visual changes but still...food for thought.
http://www.youtube.com/watch?v=THBRvtxNPvE&feature=related
Anakin Voice Change
http://www.youtube.com/watch?v=LJ0rrilAXtM
Emperor gets a more O.T. hologram.
http://www.youtube.com/watch?v=7c3tV_Qh6TQ