Allow the end user to decide what method to use for data entry when executing a command... for example, the "Extrude" command does not need both the traditional dialog box and the Mini-Toolbar. Let the end user decide by placing an option in the "Application Options" within the program.
Again, both of these are not needed and honestly make the program seem cumbersome. Please finish implementing the Mini-Toolbars so that this option is available for your end users.