Good write-up S.P.
As you pointed out I’m sure the author of the article you reference could achieve even higher MPG in a hybrid, but perhaps not enough to justify the cost. Safety is another thing that has kept newer cars from achieving increasingly higher fuel efficiency over the years. Unfortunately, as you eluded to, vehicles on the road today with are much different than they were in 1990, I’m referring of course to SUV’s and minivans. I don’t know about you but I certainly wouldn’t want my wife and child to be in a Honda CRX when and inattentive Ford Expedition, Nissan Armada, Lincoln Navigator, etc… driver who couldn’t be bothered to check the air pressure in their tires decides that checking email on their blackberry is more important than focusing on operating their 3 ton vehicle and has a blowout, misses a stop sign, or crosses the centerline into my family’s path. So thanks to that reality today all cars today are required to have a variety of enhanced safety features, such as side impact door beams, multiple airbags, seatbelt pretensioners, tire pressure monitoring systems, and soon to come (I guarantee it) lane departure and rear end collision warning systems. All these systems cost $$ and add weight.

Additionally, car manufacturers don’t spend money on research into making more efficient cars b/c it would just make their cars more expensive and (until now) people didn’t seem to care about mpg (evident by the choice of vehicles people have been making for the last two decades).

Another issue I see for why cars today don’t seem to measure up to mpg economy that was achieved years ago in similar sized vehicles is actually a misconception in some ways. One word, Speed, it doesn’t just kill people,it also kills mpg. As hypermilers are discovering, without going to extremes (i.e. pushing your car to get it rolling before you start it, shutting the car off when going downhill, and rolling through stop signs) modern cars can easily exceed EPA estimates. Tire pressure, alignment, and all of the things you mentioned in your write-up are factors, but in my experience, speed is a huge one that is often overlooked. The amount of power (and consequently fuel) required to move a vehicle grows exponentially with increased speed. The optimal speed for fuel economy is the slowest one can safely go in top gear without lugging the motor. In my unscientific observations the difference between 60mph and 70mpg in my Honda Civic Hybrid is ~2.5mpg, and the difference between 70mph and 80mph is ~5mpg.