Nice work in there!
My input to the points you raised are:
1) I do not think Arduino.cc still wants to mess around with the ATMEGA328 anymore; implement the CLKO idea doesn't seem to be the kind of effort they want to go into (specially because I see a move from 8-bit to 32-bit (ARM) and said processors have different clocking modes, some of them even work very nice with internal clocking).
2) Using linear voltage regulators is in the past now (unless they don't want to go the "extra mile" in that direction, what I find unlikely), so replacing a LDO by another doesn't seem a good idea.
3) They are already using a buck circuit on Arduino Zero, but I don't know further details about part number, etc. In that same line: what could be done is to exchange both 5V and 3.3V power regulators with buck converters (the same chip with two different outputs, perhaps?).
Regarding the "green future" you mention, I don't think Arduino.cc would sacrifice simplicity (cheap buck converters or linear regulators) solely to make a "green board"; that could be true for high-end products (Arduino 101, etc) but not for the low-end low-cost low-complexity Nano, Zero and Gemma for example. Looking at their philosophy, I don't think they put "high power efficient boards" over "easy to use" or "low complexity" ones.