Yeah, I was thinking TXB0108's and surface mount headers. What I might do is only make it only level shift the smaller pin set (that used by the Uno, Leonardo and the like) and then leave the remainder as 3.3V - with silkscreen warnings of that. As for the analog channels, I am not sure yet - possibly rail to rail op-amp circuits. I may for the analog inputs just use a Unity amplifier circuit to just protect the inputs rather.
Is there anything else that you think would be useful to have on this board?