While I am no veteran player of Twilight Imperium, from the games I've played I had mixed feelings about several optional rules, such as the Leaders and the Distant Sun tokens.
The Leaders are of widely varied usefulness, and especially the Diplomat, and somewhat the Agent stall the game.
As for distant suns, a firts-turn Radiation as compared to your neighbor's free space dock, can be a crushing occurence.
Do you use them at all, do you sort the Distant Sun tokens into low-risk and high risk?
Do you use all the leaders or none, or do you allow each player to pick one leader to use?
What about shock troops and other stuff that came with the expansion?