Okay, this project won't go any further, as I've finalized the build. Sadly, I don't have any new pictures to show, but I got a new SCPH-9002 case, that I sacrificed for the job. Repositioned the Raspberry on the case, so that it sits pretty much in the middle of the case, installed cooler with a 40 mm fan, using the 5V line from the GPIO pins, and the cooler is attached to the board with blue tac and thermal grease and used these small copper plates to lift it up from the board components. Changed the internal HDMI-extension cable to flat-type one, so it fits inside the case easily. Last but not least, got myself a Class 2 64 Gb Sandisk SD-card, that I use to store the games internally as well. The USB hub is still there to transfer games and for kb/mouse to do services.
Keeping it pretty much as simple as possible, it was a fun project to work with and has been working flawlessly from day one. I might do something else someday, as I have one spare Raspberry, maybe a retro PC-type of thing. :)