I just saw it. Dude, I just know some of you are just gonna s*** yourselves when you hear this: Hinata actually makes a reference to La Rousse City, as well as Rondo-hakase. I don't think there's anything mentioned about Satoshi-tachi actually helping to solve the La Rousse crisis (though, Masato did know what Deoxys was when it appeared, rather than anyone asking what it was), but it's nontheless further evidence that the movies might tie in with the main series. Other points include....
-It's been a while since Nyaasu was last used to speak for a Pokemon, and he looked pretty badass when possessed, too.
-Oosubame/Jukain vs. Deoxys was b*tchin' on so many levels... someone mentioned that, by going against a legendary, Jukain is catching up to Lizardon (who battled Entei and later took down a Freezer). He certainly managed to do a good job, and it's nice to see Oosubame did a bit of damage along with him (Wakashamo and Numacraw also participated, but didn't accomplish much).
-What is with Rocket Dan? After Freezer, this is pretty much the second legendary (sorta) they considered giving to Sakaki just so he could do some activity with it, as if being a extremely rare and powerful Pokemon isn't enough.
-A portal to that dimension Masato and Nyaasu were in opened up again at some point. Haruka shouts Masato's name, then Musashi says "Now that you mention it, Nyaasu!" Kojirou replies "You forgot about him?!" XD
-This is interesting. When Satoshi-tachi were blown out of that cave, Jukain was next to Satoshi to nudge him back to his senses. Wakashamo was next to Musashi, Numacraw was next to Kojirou, Oosubame was next to Haruka, and Takeshi and Hinata didn't have anyone (though, Hinata was in a crouched position rather than laying on the ground). Odd, you'd expect Wakashamo and Numacraw (especially Wakashamo) to be next to their respective trainers, wouldn't you?
-At some point, Deoxys sounded like it was able to speak without Nyaasu... to some extent. It was extremely garbled and the characters had trouble understanding, but it was clearly speaking some Japanese words. "(something something)! Mata aou ne!"