[Plugin: Shortcodes Pro] Using Shortcodes with WordPress standard buttons

You may be able to do what you want using wordpress filters

Also take a look at Customize tinyMCE with Filters

If you want to customize which buttons are shown in the editor, or you want to use a custom css file to stylize the visual editor contents, or to prevent tinyMCE from removing styles, spans, etc.. or to customize every aspect of TinyMCE, you can modify the init settings array with the use of the filter tiny_mce_before_init.

Good luck!