I have a feeling that they could go the route of DA:I Trespasser, where the Alliance is seen as the threat and we ultimately have to decide what to do with said power, because honestly the power the Outlander and the Alliance wields is rather too much.

It's happened on all of my characters ships. As far as I can recollect, it only started to happen after 4.0 went live.

I think this more to be an uneasy alliance against a threat to both major power players. Once the threat has been resolved, the Republic and Empire will most likely revert back into war.

Coming from someone that has always been full-Pub side for anything in the SW franchise, I have to say I am surprised at how much I enjoy playing as a LS Sith Warrior. He has his moments of darkness sure, but so far it has been very enjoyable and the characters are more fleshed out and realistic (plus Vette is awesome!), though because I tend to like clichéd storylines I enjoy the JK more, but only slightly. Give the SW a try, I think you'll be surprised.