Theory and conjecture aside , I have seen real world success in teaching problem students on three channel birds .The main thing was , after months of trying they quickly sloloed on a three channel plane with minimal coaching. Once they gain confidence and become comfortable with take off and landing it is so easy to move the rudder to the other stick .
BTW: The Bridi Trainer series turn well on rudder , as does the current Toledo Special !
Heck , my first plane had a single channel , no elevator , ailerons or throttle .

You can learn either way but there is certainly nothing wrong with learning on a three channel setup.