There are various option when it comes to connect RPI with external embedded boards. Currently many geeks are trying to interface various peripherals with RPI with the I/O header given. I feel there are following option one can go with.
1) Use I/O header.
Which i feel is good for prototyping but as we move do something that looks good this option is not what I feel is best, I hate all the wires that comes out of RPI and then loose connection and what not to take care of...
2) Use of USB port.
RPI is computer and you it can communicate to co-processor using its USB ports.I think this is very neat way to do things. For example if you are making a robot which has a microcontroller that has UART it can easily communicate with RPI above that you can reflash you microcontroller as per your application using RPI. I know there are no instruction or related work out there like this but soon i will be posting instruction to do this on my blog as well on code exchange.
Would like to now community views on same.