Panels standard renderer has very flexible undocumented feature of controlling the sequence of panels being rendered.

By default you have possibility to use 'render first' and 'render last' in your content type definition so you already can control what pane should be rendered for example last. Undocumented part is more interesting that is hook_panels_panes_prepared_alter() that runs after all panes were set up. So you can alter the array of panes in which way you can control sequence of panes being rendered. This feature is super handy when you have dependent panes.