I've got a timecapsule (4th gen) and ran initially into problems (with AFP giving even worse results than SMB). Those seems to be solved by changing TCP ACK settings in sysctl.conf on the ATV2 :
Note that the value "0" simply don't work.
Playing high bitrates 1280p mkv now works like a charm with AFP - occasional stuttering may appear with SMB, but it is ways better than before (systematic buffering). Using Wifi.
Worth a try i think.
Sounds like we're on to something here!