They could've spiced up Volcanion and The Mechanical Marvel if they really wanted to.

They could've made all of the Pokemon the villains end up with be stolen since they're all being controlled with the mega wave thing anyway. And then just to spice it up even more, make all the Pokemon species they have and Ash has/had be stolen from Oak's (Or Viridian Forest if you're Pidgeot) and be Ash's.

Could have had them fight even harder against the Mega Wave thingie and actually not get controlled by it when they see Ash. They could've stolen their Pokeballs back and gave them to Ash. Maybe he would've only sent the Pokeballs over to Oak's lab until the end of the movie when they get sent back so Ash can continue in Kalos.

Since Team Rocket ended up with a Heracross (and a Pinsir but that's not important) they could've been like "huh, this Heracross seems familiar." and Heracross could've been using Team Rocket to find Ash after being handed over to them since he knows wherever Team Rocket is, Ash can't be that far away.

Honestly, I've thought about writing an actual story about this for a while now. I'm still on the fence.