I have now been playing this game at least 20 times, half of it with the expansion. With my friend, we have added a few minor house rules. I wanted to post those here, as well as get feedback from anyone else about their own preferred house rules suggestions.

Setup (RotE p1)

Prepare objective deck
House rule
"V. Randomly pick three of the unused objective cards , one from each stage, and show them to all players".
reasoning: For the Empire, knowing one of the objectives at each tier that will not be a potential risk during this game reduces a little bit the significant impact RotE had over the ability of the imperial player to try to prevent objectives conditions, when the game had no discarded objectives cards pre-RotE.

Place starting Units and Loyalty
Current rule
"players must agree on whether to use the starting unit from the base game or the RotE starting units"
House rule
"Imperial player decides for both players on whether to use the starting units from the base game or the RotE starting units"
reasoning: This decision is significantly more meaningful for the imperial player than for the rebel player.

ERRATA

Current rule
"If the Rebel player wishes to optionally reveal his base, he can do so at the start of one of his turns of the command phase, before using one of his leader"
House rule
"If the Rebel player wishes to optionally reveal his base, he can do so at the start of one of his turns of the command phase, before using one of his leader, or when the imperial player decides to retreat in his hidden base system, revealing the units there and preventing the retreat in that system."
reasoning: being able to move a fleet in two different systems in one turn to reveal the still hidden base and possibly bring ground units there thanks to a "retreat" is too strong of a capability for the Empire. The retreat move would still reveal the hiddeb base, but prevent ground units there this turn if the rebel has any units left in the base.