I am thinking of just wiring the USB cable directly in instead of having the connector. In this case would it be more beneficial to layout if the mounting holes and pads for the USB wire were in different locations? For example, keeping the voltage and ground USB wire mounting holes closer to the PIC itself (PINS :31/32 or 11/12), and the data lines closer to the pins on the PIC itself (PINS: 23/24). In most USB boards where I have seen the USB cable directly soldered to the board and where they have no connector, the pins are in a a row, and not spread over the board. The layout may be a bit easier if I choose the mounting holes for the USB wires to be closer to where they need to be routed instead of putting them in a row, and routing them to the PIC's pins.
I have considered using a smaller PIC after I have tested on the 45K20. This seemed to be my cheapest option, and will be easiest to prototype with since it is a DIP package. I was thinking of adding an ICSP female header to come out the back of the device in my prototyping stages that way I could just plug my PICKIT3 directly into the female headers using long male header pins to bridge between the PIC's female header and the devices female header. Thanks for pointing out the 10K for the reset. I have a feeling that there is a lot that I could change on this board/schematic, but I threw it together in a few minutes the get the idea on "paper". I have yet to receive my PIC45K50 chips in the mail, but they are on their way from Thailand. I am considering replacing the entire board on the NES controller with a full fabricated board solution as well. If I am going to put in the time I would like a nice product in the end. I quite like the feel of the original NES controller so I am sticking with that case. Does anyone know how to layout traces for push buttons that work with that rubber (capacitive?) material. I kind of want to build up a solution where you could just take out the existing NES controller board, and replace it with this custom solution. It seems like those board's days are numbered.