I personally am a fan of the 25th anniversary color scheme if you are sold on painting it. It has a classy look and is already calling back to the original famicom colors, so I think that tribute is a nice choice.
You could also look into retrobight and maybe be swayed back to going stock.
Looking at the Nintendo cartridge conversion, do you plan on having it removable, so you could switch out the OS with a cartridge (hard drive) swap. Have one cartridge be XBMC, another Hyperspin? That would be totally awesome! Maybe then you could make custom labels for crappy carts that say "Hyperspin" or "XBMC" on them.
Also, awesome work! I would have made all the same decisions if I were doing another build now. The build I have on youtube was built so long ago that using the original RCA connectors was a good decision then, and helped with the stock look, but today that would be a silly choice to make again. The HDMI makes much more sense.
Finally, welcome to the forums! It's great to have you.