For Milotic's "Aqua Swirl" attack who gets to choose which Benched Pokemon becomes the new Active Pokemon?
First off, since the attack says "you may" the attacking player gets to choose if any switching happens at all. Then if so, the opponent gets to choose which the Benched Pokemon becomes their new Active Pokemon.
Source: Primal Clash FAQ (2015-02-05), TPCi Rules Team (2015-02-05)

Relevant cards

Note: All applicable cards may not be listed below.
XY5_44