Next beta version will have ability to set higher MTU for ethernet card that support such feature, for example, some Intel Gigabit cards.The routing does add a penalty.
I am currently hoping mikrotik will add oversized frame support for their ethernet cards (and my favourite brand Intel). Intel cards atleast can send ethernet frames up to 2000 bytes in size (and so can many others too). Most mid-level to high-level switches support forwarding over ethernet frames up to atleast 1600 or even more.
If this support was added to Mikrotik RouterOS we could run networks where EoIP would be even more efficient.
Most carriers (around here atleast) support larger frames so they can use technologies like QinQ, MPLS or EoIP like protocols.