In the meantime...
Runaway: "J'aime ton odeur."
And I'm still trying to think of a way to introduce Trak, and a good opening to do so. Being a Kalos Hall of Famer, she'd have some notoriety, along with using Mega Evolutions (Runaway being her main 'mon), so there's that. I'm considering leaving out the Team Flare stuff, in case they become a plot point in a Kalos quest.
Her experience with Mega Evolutions would be beneficial to Team Flora's plans, as Mega Evolving a Venusaur could produce a more potent Stun Spore formulation. That link of having her be brought over from Kalos by someone with a link to Team Flora was my main method of introducing her. However, Trak has researched other Teams, and thus a Team Anything would raise her hackles and she wouldn't knowingly participate in anything.
Thus, having her be brought over under false pretenses would work better. Heck, she could initially be at odds with everyone else, as she's defending her regional sponsor, not knowing their true intentions. Wily's dual identity could work well in that favor, as I doubt he'd be the type to broadcast his affiliations even when evil.
That would make for an interesting conflict, as our heroes could initially be forced to battle her and Runaway.