Two Different Crystal Resonator on Arduino Mega?
The ATmega16U2 uses a quartz crystal because it needs a very accurate and stable frequency for USB. The ATmega2560 uses a ceramic resonator which is less accurate, but cheaper (lower unit cost, fewer parts, smaller board area).

If saving a few cents isn't important then you could use a quartz crystal for both MCUs. This would make your board more suitable for applications requiring high accuracy, eg. a real-time clock or frequency counter.