I have the same problem, found if i holster my weapon then redraw it they will equip their weapons..have to keep close watch tho cause changing zones undoes it.
same issue here error 36 file is locked that cannot be opened and just keeps restarting over and over without success..download of patch never finished because some file is locked up..game won't run.
The story doesn't change no matter which side you choose, differences will be in ship selections, costumes, consoles availability..re: plasmotic leech. I prefered fed side as my fleet was fed based..