Being a recent CR-Z buyer (and probably the only one on this forum), I'll attempt to explain some of this
I will first state, that I have no misconceptions about the CR-Z being fast. It does reasonably well on a mountain road, the main limitation being the tires. As stupid as it sounds, putting it in sport mode really improves engine response. But 95% of the time it doesn't matter since I'm stuck in traffic or cruising at freeway speeds. To be fair, there's no way I would have even considered the car if it didn't have a 6MT.
Through about 1500 miles I'm averaging about 38-39mpg in mixed driving; my daily commute is almost exactly 50/50 highway and surface street.
It is rather small, but why do I need a bigger car for commuting? For times when space is needed, we use my wife's WRX wagon.
I don't really see $20k as being terribly expensive. Yes, I could have gotten a Civic for similar money with a bit more "stuff" but honestly this was more comfortable. I did look at a Focus for similar money but had to sacrifice options to get an MT, which is an absolute requirement.
So really, the CR-Z is without question a niche vehicle. Even Honda has stated a modest sales goal of 15k per year.