If you rest your shoe on the L model's dead pedal, it constantly gets caught under the clutch pedal, and you end up having to hover that foot above the clutch when you anticipate a gear change soon.
The gear shift feels very crude and notchy.
Stick shift does yield more zoom-zoom over automatic, but the LE model with automatic shift and more creature comforts - such as power windows - will make your drive more enjoyable.
I had an LE model in 2006 which easily survived being T-boned in the driver door by pickup truck, and I traded it for a VW Rabbit.
My 2012 L stick easily yielded 32 mpg in short city drives, but after 5 months I'm dumping it for a great Mazda3 iTouring hatch.
Small size; cute, modest styling; tight turn circle; good cargo capacity with rear seats down; good seats.
The Yaris is a great driver, primarily with auto shift and power windows, etc.
The L is just too "basic" for real enjoyment, and the price saving over an auto shift model is not worth it, in the long run.
The manual shift in the L model is no joy because the footwell is too restricted, lacking room between the dead pedal and the clutch.
When shifting, the gear stick action feels very crude.
The footwell is the same size as in the automatic shift model, and is just too much a pain in the stick model.