Is the CRZ still available to you guys. It is available with a manual, but it isn't the most frugal hybrid. Honda's new one motor system is a dual clutch transmission, and I think the Jetta hybrid is also.
The real efficiency sucker on an automatic is the torque converter, and on those hybrids still using a traditional CVT or step transmission, the torque converter is replaced by the electric motor.
On most of the high efficiency hybrids, the transmission is the hybrid system. The Toyota and Ford system is a single planetary gear set with no clutch. They mechanically simpler, and more efficient, than a manual. Honda's two motor system in the Accord hybrid is simpler still. With just a fixed set of gears connecting the motor to the wheels that the engine can clutch into at highway speeds, Honda claims it doesn't have a transmission.