Do some searches for firmata.
It allows a host to manipulate the Arduino pins as well as read their inputs.
There are packages/libraries out there for languages like python as well as a few others
to make it quite easy.
When using firmata you can connect to the Pi using USB so you don't have to mess with
any connections to the i/o connector or have any 3v worries.
If you want to go the Firmata route, the Teensy (http://www.pjrc.com/teensy/
a great external i/o interface for the Pi since it uses native USB which is fast and
won't suffer character loss like the standard Arduinos which use a USB to serial chip.