Wood and I are going to be TR, that's what we were in PS1 and that's what we'll always be. Planetside does a very good job in instilling a sense of faction pride and loyalty. As for your question, I believe that's something that is still up in the air and will probably get hammered out in beta. How it was in the first game originally is you could only have 1 faction per server. Later on when they started merging servers they realized they couldn't do that anymore because people would have other characters in the other factions when the merge happened, and they didn't want to just lock those characters or delete them. So they went with a lock out timer for switching empires. Example: If you logged in on a TR character, then changed your mind and logged onto a NC character, you would then be locked from playing anything but NC for 6 hours. The reason for the lock was to deter people from hopping on the opposing faction, getting their battle plans, then switching back and rofl-stomping them. People still do it, but it's just rare.
Being that it's going to be free to play, SOE does know that some people will probably make multiple accounts anyways, so I personally don't see the reason for 1 faction per server. How it is in the last builds we've seen from E3 and stuff, is you can have all 3 factions on 1 server. We'll see if that changes in beta.