The Evo has speed control on the flap and spoiler functions. It has shift select for the USA.
Evo has optional synthesiser, frequency scanner and channel check, though I don't know if the frequency scanner and channel check are available on 72Mhz.
Afaik the JR does not offer synth modules yet, and for the foreseeable future will not offer scanner and channel check. Evo is designed to allow programming of numerical values in flight.
Evo has plenty memories on board, the PC software to backup the Tx is free all you pay for is the cable.
Evo can have sticks with switches/buttons on top, for thumb and finger fliers.
Evo's downsides are the slow transition between flight phases which is fixed at the factory, and lack of expo per flight phase which is not good for 3D fliers.