The reason I left in 2009 or 2010 is because of the negative atmosphere. It was a time of huge turmoil. Groups were getting flamed with a new thread every day, vets were making groups of ridiculous characters simply for PvP (i.e. the 'Al Qaeda' [hello, NSA] faction), and most of the aforementioned vets were trolls to boot. They got away with +1'ing in threads with serious discussion potential by posting inflammatory things. If you called them out on it, you derailed the thread. If you didn't they got away with being a jerk.
To some extent, I see that negative atmosphere still. People are too quick to judge one another. The problem with a roleplay server is that everyone wants to be the best storyteller, and with that comes ego, and with that comes the notion that people can get away with being a jerk.
We forget that there are other human beings on the other side of the screen, and our pride is quick to say, "What an idiot you are for this suggestion!"
We need to remember that we're all human, we're all trying our best. If you disagree with something, say it in a rational manner.
-Edit- Also, for me, once the move toward forming 'generic' factions was made, a lot of RP potential was lost. The Southern Alliance became the Liberty Navy. The Black Squadron became the Order. Queen Carina's Own became the BAF. I understand the importance of sticking to vanilla lore, but when you eliminate special groups like that in favor of generic roles, you eliminate roleplay flexibility. Special groups can have special goals. Generic factions can only hope to shoot the enemies listed in their info card.
In many ways, we did to factions what we should have done with systems. Simplification.