I totally agree. Not because of any role-play/PVE aspect, but more about the PVP aspect. In factioned PVP, it becomes stale with only 2 factions. It's much more exciting with 3 factions and allows for more dynamics. Not too mention there is less chance of one faction outnumbering the other.
Yeah, my guildies were just talking about this. DaoC, Vanguard, had 3 factions and worked much better for factioned pvp.
Who knows what Bioware will do later on. But I vote for a Neutral/Merc/Hutt faction with Rodians, Mandalorians etc and just choose which faction you want to be in.