It's an interesting exercise, although the first downside I noticed of the "one file" mantra is that all of the CSS is served inline in every response.

Also, you may want to consider handling MySQL errors in a manner other than just printing it to screen along with the query. At the very least, log them somewhere where you'll be alerted of the error. As a user, seeing "MySQLi Error: [...]" doesn't help me or you.

It'll be interesting to see if you continue the project and how far you take its functionality. Some of my co-workers were just today discussing the tendency to want to rewrite a system from scratch in order to simplify it and avoid any problems with backwards compatibility, only to slowly find yourself rewriting the "unnecessary" features from which you were trying to escape.