Connection between Cyclone III with ATXmega or HC series logic device

I suggest you don't over-complicate it with a buffer.

If you're concerned 120 ohms is too low, by all means fit something higher. When it's working as intended, one device will always present a high impedance, much higher than any (sensibly chosen) series resistor. Thus 1kR, or even 10kR should not prevent it working and protect you very adequately from both devices driving opposing logic levels. The only time this may prove to be a problem is if your board traces are long, resulting in a relatively high trace capacitance. Thus, with a larger value you will end up slowing all your edges down.

Cheers,

Alex