During my recent Webinar on understanding SharePoint Content Types someone asked me if he should use Content Types or save the library as a template. He also wanted to know the differences between the two.
When you save a library as template, you lose the ability to centrally manage it afterwards. In this example, I take an Invoice Content Type vs an Invoice Library saved as template. With an Invoice Content Type, I can centrally manage the settings and the columns even after the libraries have been created whereas with the saved as template it is too late. My recommendation is to create the SharePoint Content Type and assign to a library that you will then save as template.