Seems to me a simpler solution is to develop a standardized pinout for the mcu + minimum parts and prototype pcbs that take the standardized pin out. So you simply insert a this "mcu board" into the prototype pcb and you get different kinds of avr/arduino board.
The mcu board should just contain the mcu, (optional) oscillators / crystals, and pin outs. You can make it based on lqfp48/64, depending on the largest mcu you want to incorporate. The prototype pcb would supply power.
Thanks for the input. Having the option of choosing different MCUs is an interesting idea. However, I decided to go with the 328P because it is the most compatible MCU with Arduino projects makers have built around the world. Although it may be a good idea to design at least one board for an Attiny and one for a big, 64 pin, Mega.