I read an article recently called "Thinking for yourself in your context" is the heart of Lean. It stated that better efficiency in software development would be achieved if workers had shared goals, and that these goals should center around why you are implementing a feature rather than just how to do it. The point is that people should step back to understand the whole picture and use that information to inform their decisions. That is why a kanban board for a team is so important. It keeps everyone on the same page with a project, so they can stop focusing so much on the how and really focus on the why. This is definitely empowering to employees. Though empowerment can be a good and bad thing for the team, employees will appreciate the ability to "think for themselves" in the long-term. 

We built flexibility in to Zen to try to empower the team to use the product in their own way, but because there are so many ways to make Zen your own like coloring stories, tagging, etc., there can be some growing pains as you figure out the best way to use the software. In the end though, members of a team will appreciate that they are able to make the decisions rather than having unnecessary restrictions placed upon them. We have a documentation section on the homepage of each project, so that you can document the way you use the software and keep every member of your team in the loop. We will also be posting soon on how we "dogfooded" Zen to create Zen and how we continue to use it to manage the product. This may give teams some additional ideas about what might work for them.