I did the flashpoints on Ilum (Battle for Ilum / The False Emperor) and I feel a bit dissatisfied with what happened to Malgus. To be honest, his new ideal Empire was one where I would actually like to have a character on or belonging to. I played through as the Republic during the beta and launch and saw no changes made overall. I have yet to look into the Imperial's view, but is it really for the better?
Is the fact that he wants an Empire composed of all sentient life too hard for the current Empire to take? Or is it something else?
Scene for Republic: http://www.youtube.com/watch?v=75q8TpOV_pI