We don't know anything at all about SWTOR's PvP features yet, but we're eager to assume that there will be some kind of large scale faction-on-faction conflict. If it's Empire vs. Republic, though, won't that good guy in a bad place be forced to fight against his fellow Jedi? If it's Jedi vs. Sith, how will the prospect of killing a fellow citizen be handled? If it's both, we can imagine Sith members of the Republic turning on teammates because they are Jedi. Yikes!
Furthermore, we're curious as to whether or not players will be able to switch sides on either spectrum -- can Jedi become Sith and vice versa? Can players defect from the Empire to the Republic? Players of the Star Wars: Knights of the Old Republic might remember the old Jedi Jolee Bindo, who was arguably a nuetral character who did not completely subscribe to either extreme of the Force. Will there be a role for players who want to walk that middle ground?
The game is at such an early stage in production, it's possible that even BioWare doesn't have the answers to all of our questions yet. We're always eager to speculate though!
In a video interview with GameSpot, BioWare reps suggested that a tenuous peace has been reached between the Empire and the Republic. That might sound like it means there will be no direct military conflict between the two, but similar language has been used to describe the relationship between the Horde and the Alliance in World of Warcraft.
Some past games have balanced multiple conflicts with messy boundaries -- EVE Online now features factional warfare in addition to its traditional corporate conflicts, and Meridian 59 has long juggled faction struggles, guild wars, and for a while in its history, a war between Jedi-like Hunters and Sith-like Necromancers. That means it's not impossible, but those games are a bit more hardcore in the PvP department than most gamers prefer, so we're not sure it's in BioWare's best interest to adopt their approaches.
With Warhammer Online's focus on PvP, it would seem that the tide is turning more in that direction, so we've got to assume BioWare has something planned. Right now we have mostly questions though, and no answers -- we're taking bets on how they're gonna approach it!