Physical interface MTU/L2 MTU should be maxed out on all physical ports identically.
L3 MTU on all physical interfaces and bridges/wireless bridges should be 1500. But if you’re running tunnelling protocols like VPLS, L3 MTU = 1600.
If you’re using /interface vlans on MikroTik, L3 MTU on it should match 1500 or 1600.
More details here on the MTU section: http://forum.mikrotik.com/t/how-to-edge-router-and-bng-optimization-for-isps/150007/1