Here is my thought, and I could be digging myself a huge hole. That's why I'm here ;)
I am looking to develop a complex application but I want this application to run both as a standalone script as a wordpress plugin. Later I may develop into a Joomla plugin and so on.
My thought is I develop an abstract custom framework and then implement the custom functionality via extending this framework. Does that make sense?
My_Engine, and then that plugin class will act as factory to manage the custom functionality in the WordPress
I really don't want to have to repeat myself and I would definitely be producing multiple versions of the app.