You should definitely ALWAYS go Q first, the Cooldown reduction on isolated targets is huge and cranks Kha's damage potential up a huge amount making for a great level 6 powerspike and huge dueling potential.
E/W second is a matter of personal choice, If their team is staying grouped up more by the time you hit level 11 W is probably better because you are less likely to be able to jump in and assassinate a squishy to reset E and jump back out.
Honestly R is kinda the most worthless one to evolve, its evolution does not give nearly as much power as the other 3 do to their respective abilities, and in general R is used before jumping in for an engage, or to get out after a disengage, and 1 extra usage of this is not going to help that much.
Imo you are definitely putting yourself at a heavy disadvantage by choosing to evolve R at all rather than your other abilities.