This seems appropriate given today's news of Trello investment. Trello is a good example of a product that is not necessarily simple to use for any specific use case, but it's very easy to adapt to your needs, and leaves you in complete control over decision making. To echo gigawhat's comment, one could compare Trello to a manual transmission, and tools like Pivotal/JIRA to an automatic one.
An even better real-world example might be manual transmissions, which are now both slower and less efficient than modern automatic counterparts. Some people (like myself) prefer them regardless.
They are pretty standard here in Europe. It takes more effort to learn, but not much once you have learned to use one. I guess I feel the same about Linux. More effort upfront, but far more control afterwards.