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GPON is more efficient than an EPON when running GEM mode. GEM is essentially GFP over PON. Its nice and works well for Ethernet transport. GPON in traditional ATM mode is no different that APON/BPON and carries all of the ATM overhead and inefficiencies and is much less efficient than EPON for Ethernet transport.
The Ethernet protocol legacy was carried over to EPON for a number of reasons. Probably the most important reason is that it allows vendors to use standard Ethernet pieces when building EPON chips/ONU. This has allowed for relatively inexpensive EPON ONUs. In Japan the EPON ONU price is under $100.
As always, Ethernet is less efficient but cheaper than ATM based systems. In addition, GPONs attempt to resolve everyone’s problem has made it overly complicated and, at least initally, more expensive. Pick your poison.
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GEPON vs. EPON