I expect it's something we'll see eventually.
(1) Flag self as available for PVP
(2) Choose League(s) interested in playing
(3) PoGo prompts "A challenger appears!" with the league to be played
(4) Both players confirm
(5) Pre-match starts -- pick pokemon
(6) Match starts
(7) At the conclusion of the match, PoGo prompts if you want to play again
(8) If both players confirm, go to Step 5
(9) If one or both players decline, return to PVP queue. Perhaps a short cooldown so that PoGo doesnt try to match the same two trainers immediately
It's kinda clunky, but it's a start.