Is there a proper, pluggable way to create a GUI for shortcodes in TinyMCE (Much like the insert link sidebar)?

I found an example here http://chillburn.com.au/demos/code-differences-wysiwyg-editor/ that seems to be on the right track, but requires modifying the core files, which doesn't seem like the best route.

Creating the TinyMCE plugin with button is easy, but things get murky due to the hard coding in LeftAndMain.ss and HTMLEditorField.php

Is there a best way to add a new right side element?

Ultimately, I'm looking to create a rightside selector for files, that uses ID rather than simply embedding the path in an href.
This would allow the shortcode to display more of the file properties, such as size, date modified etc.

Thanks in advance!

Unfortunately there isn't an easy way to do this - I once looked into creating another right side panel but gave up pretty quick. That is getting an overhaul in SS 3 (see design here https://github.com/silverstripe/silverstripe-design/blob/master/Design/ss3-ui_insert-link.jpg) but I'm unsure how they are implementing it and how pluggable it will be.