I've done a decent amount of work with AVR based systems (built several 3d printers as a project over the last few years, now i have a bike to focus on.)
the RBBB is from moderndevice.com originally. i've used several (and a couple of BBBs too. larger formfactor, but easier to plug in some things like servos) there are also tons of sensors on there too, but i couldn't find any accelerometers that happen to be I2c, which might help with the lack of pins thing. otherwise, you can always push up to one of the big brothers. sanguino, arduino mega, etc. same programming interface, so it doesn't actually add any complexity, just size, unless you go for surface mount versions on a custom board.
let me know if i can help in any way.