I do make my own Arduino Board for RaspberryPI before. But it make from prototype board and have a lot of cable. I like that but I still not able to put a Arduino shield into my DIY board.
So, this is my solution. The AlaMode. It have RaspberryPI GPIO port, Arduino Shield Compatible port, DS3231 (Precise RTC), Logic level shifter, SD Card reader, FTDI port. And it use Atmega 328p ZIP socket.
With bundled software from developer website. You’ll able to program Arduino board directly from RaspberryPI (via Serial port).