Like most things there are pros and cons.
- Pro: More gear ratio options allows a better ability to convert the real time road torque and RPM situation into a combination that is at more efficient point on a ICE's BSFC.
- Con: Manual transmissions has a loss of efficiency during the shifting period ... the more one has to shift the more shifting losses... more gears means more shifting over the same RPM and torque transition.
- Pro: Manual transmissions can be more energy efficient from input to output.
- Con: Finite Manual Transmissions have fewer gear options than other 'CVT' and the like ... ie they are less able to have the 'best' ICE gear ratio for all road torque and RPM conditions.
I have a interesting paper about the efficiencies of various transmissions.
Sadly it is not free...
Link
But ... here are some teasers / interesting bits from the testing in it.
PumpCVT
Manual
Toroidal
BeltCVT
BallPump
FixedDisplacementPump
Automatic