Perhaps the main problem with being a member of only one faction is that it can limit your long-term perspective.
I joined up with the Congress around September, and've been with them since, with a few months off due to computer problems.
This means that no matter what angle I look from, nothing really changes; the pigl--er, Hogosha (typing that insult's become almost automatic now) and the Xenos are always the enemy, the lawful forces are always something to keep an eye out for, almost never a source of aid, and the Rogues and the like are almost always an ally, not a pirating menace.
When you don't have to go through the reality check of changing perspectives, and completely switching around your alignments, on a regular basis, it can get pretty easy to associate specific players with 'the enemy'. Clearly, in a sense, we're too personally involved with the game.
We do hate Yarr, but after fighting him enough in-character, to be honest, because of him, we may not be all that fond of you either.
This is an area that some of us may have room to work on.
These and the other issues have been discussed internally and will hopefully not recur; thanks for your input!