There is a great series of articles being written by Derek Powazek at the moment: Things I Learned the Hard Way. This one is particularly relevant to me at the moment, dealing with systems that involve change and change of some long-standing behaviours. Hopefully this well help me / you see beyond the complaints to the actual reasons behind them.
But he has taught me a few things, and one I keep coming back to is: ignore the content. Sometimes, when dealing with an interpersonal conflict, logically addressing the complaints is that last thing that will help. Instead, try to address the emotion behind it.