@ratedrguy It depends on for you want to go with the port. If you want all the options the original offers, the best way is to use some sort of config.xml with the includes. Then it would be easy to manually change certain elements.
If you only want one particular layout for the carousel and/or game views, I suggest not to use includes at all.
But yeah, trying to completely start from scratch would be a good way to start if you are new to all this. EmulationStation themes are very restricted and therefore quite simple if you know the basics.
When you got into it, you can later copy the settings from the original (mainly size and position) to your new theme.
That's at least how I got into it. Back then there was no theme that I really liked. One had a good looking system view but awful looking game views or vise versa. Then I tried to merge themes. To figure out what element does what, I made some small changes to the positions and checked what changed.
Another minor suggestion is to work on the text elements first (without defining a font path) and add images afterwards and then add fonts and fix the sizes/positions. Wrong paths are the only thing I know of that can crash EmulationStation. By adding those at late as possible, you can tell that your initial layout code is correct.
Edit: I think I know why your theme falls back to the default settings. Your nes/theme.xml is missing the include to the root theme.xml.
Since the nes/theme.xml has the highest priority all settings from the root theme.xml are not applied.
