I also often see a lack of integration of the management process and the functional activities within an organization. Look at the criteria and ask what's in there that isn't important to their organization. What they'll soon realize is that it's all important. They have to develop their people, to satisfy their customers, manage information well. They have to do everything in there and do it well.
Some small companies think the contest criteria are stacked in favor of large organizations.
I was involved with the Baldrige from the beginning. In 1988, the criteria were written by people who came from primarily large manufacturing organizations. The Baldrige staff has worked diligently to refine and improve the criteria. You're looking at the tip of the iceberg. Most companies we work with don't have any intention of applying.