I invite those that are more knowledgable on these cars to chime in.
The 2006 hybrid Civic is a excellent and selling well. In fact, it was Motor Trend's Car of the Year. From the perspective of a number of people here such as Dan, there were some tradeoffs.
In the redesign of the HCH II, the five-speed and lean burn was thrown out - not an option.
The combined FE of the latest Prius is 55mpg, the HCH II is 50mpg, the last HCH I is 48mpg.
The impression I get of the 2006 hybrid Civic from a fuel economy standpoint is "thrre steps forward - two steps back". The improvements to the engine and electric motor were greater than the loss of lean-burn and the five speed. Leads me to think the 2006 hybrid Civic might have matched the Prius' EPA 55mpg if it was an upgraded HCH I 5-speed. Did they also increase the performance on the HCH II over the HCH I?
Said this before, I understand why Honda is getting away from hybrids with manual transmissions. It's just too easy for people to lug one and deep discharge the hybrid battery pack. Even though this is the driver's fault, it's bad business for Honda not to assume responsibility, so the obvious way out is to only offer hybrids with CVT transmissions.
I love 5-speeds. I don't hate CVTs - just unfamiliar with them. I do like CVTs over fluid automatics.
I just hope Honda will be more competive with Toyota in the future. At least they are not GM.