There was a write up in the Providence Journal by one Maurice Webb (rocket scientist/combustion specialist) who argues that the higher density of gasoline vs. ethanol effects ultimate performance comparisons of the fuels as the fuel-to-air ratio for complete combustion of gasoline is higher than that of ethanol.  

To my understanding, this means that more btus are needed for max. temp and optimum combustion thus efficiency of gasoline as a motor fuel then ethanol.

And if that's the case, could engines not be specifically designed to run on E100 thus overcoming a large portion of the BTU deficiencies you oft mention?

AFAIK, there are just two design parameters that need to change to go from gasoline to E100:
  1. the fuel-air ratio;
  2. elimination of any plastic/rubber components from the fuel system that may be attacked by E100.

The second issue is obviously the more difficult design change. A modern engine can probably change its fuel/air ratio with a simple parametric tweak to its software.

Also have to deal with vaporization or atomization issues of ethanol at cold temps, the fuel must be preheated a bit, just like in an alcohol stove. Im sure fuel injection helps a great deal with this, but for small motors injection isnt always practical. IIRC the change in fuel-air ratio is big enough that your average run of the mill production car fuel system might not quite be able to have enough volume to be ok with just a software change, depends on how much "headroom" the engineers left in the system.
AFAIK, there are just two design parameters that need to change to go from gasoline to E100:

I think the most important is the compression ratio. Increasing the compression ratio has been shown to improve gas mileage of E85 vehicles. Instead of a 25% drop in fuel efficiency, they only have a 15% or so drop.

25% and 15% per gallon though.  What should we look at it we want to judge ethanol vs gasoline as a automotive fuel ... miles per Calorie or BTU?

I'd think we'd want to know the conversion efficiency from chemcial potential energy to practical kinetic energy.