From what I've read, your water/fuel seperator won't work with ethanol because ethanol mixes with water. In fact ethanol is quite hydroscopic...it will absorb moisture right out of the air.
I agree, moving to a high or all ethanol fuel could really create issues for us boaters. Both 2-strokes and 4-strokes should be modified to effectively run on ethanol. Without modifications, our motors will either run like crap, ethanol being about 33% less efficient, or not run at all.
4-strokes are an easier modification because they use a carburater that can be more readily adjusted to compensate for the richer running, less fuel efficient ethanol. Basically the air to fuel ratio needs to be adjusted allowing more fuel to enter the combustion chamber.
2-strokes present the biggest problem with their fuel injecters. The sensors need to be reprogramed for the higher ratio, something that requires special equipment, would prove difficult to accomplish in a retrofit, and be very costly. Also, the standard 2-stroke oil doesn't mix readily with ethanol. It has been proposed that Biodeisel could be used as an alternative to the traditional 2-stroke oil but limmited studies have been done.
Then you have all the other issues associated with it being a more aggresive solvent that may require new hoses, fittings, and tanks (if fiberglass)....to say nothing about it solvating the sludge at the bottom of my 18 year old boat's gas tank and fowling up everything.
If it goes this way there's going to be some bumpy roads ahead for us boaters and the boating industry in general.
Guess my next motor won't be and E-tec. Frankly, it kinda makes sense to hold off on buying a boat/engine until this sorts itself out and the actual manufacturers get on board.
PS: I just re-read my post and I sound like chicken little. Hope it doesn't happen as I predict.