It doesn't really screw anything up. I would guess some people are disappointed because they wanted something else (new mechanics, imperial huge ships, tie advanced fix, etc.)...
Can some please point out to me exactly how a 3rd faction £#~!{¥ up the game on the tabletop?
It's not like the "ships are from 2 different eras in the timeline so you can't have a Naboo Fighter vs a TIE Defender(despite the fact it's only been like 20-25 years or something between the end of Episode 3 and the end of RotJ in a universe where light saber tech is like 1000 years old or more). I doubt you'll be able to have a combo of Rebels/Imperials and pirates as a fleet in anything but maybe epic play and even then if it's ok with your opponent.