Seeing Palkia and Dialga working together to help protect Pikachu and Piplup from the space destortions. It's nice to see they no longer hold any animosity towards each other.
Ash and Pikachu stepping in to try and save Dialga from Giratina after Sheena's attempt fails. Ash calls out to the beast, and Giratina's anger vanishes when it sees him.
Both of Arceus's goodbye scenes.
When the gang finds the stone plaque written by Damos. That part can make anyone a little misty-eyed.
"To all of my beautiful future children, who taught me how to believe. I offer you now all my sincerest hopes and wishes. That the future world will become more and more beautiful. And that is exactly the kind of world, you find yourselves in."
The cameos of Newton visiting Zero in prison, having recovered Infi's data from the previous movie. The look on his face sells it.