Marcel van der pol
So as far as I know/understand the only known information before unit setup are the unit counts, which systems are loyal/subjugated and the Rebels have 1 objective card in their hand.
Correct. The Empire doesn't know which systems are loyal to the Rebels when he deploys his units. The Rebel (going second) would however know how the Empire has deployed his units.
The 2 things that I feel could really affect your initial plan is if you got your 2 randomized mission and action cards before.
I haven't really tried it, my opponent has accidentally drawn the action cards before(so i did as well), but they were of the boring kind - we didn't reveal the immediate ones until after unit placement.
has anyone else?
It could possibly affect the way you place your units. However, since Fleet movement is rather slow, you also need to take the long-term view when deploying units. I rather doubt that knowing the two starting missions before deploying would severely change my unit setup.