( FNAF3 Spoilers! )
I'm pretty sure it's just me, but I noticed that in certain Pokemon movies (and even games, if you think about it) that when a dysfunctional and/or tragic yaoi couple is thrown in as a catalyst to the plot, the story gets a whole new layer, and sometimes even immensely
improves. For example:
1. The Lucario movie is not only about healing old wounds and helping ghosts rest in peace, it's the tale of a star-crossed couple who are reunited after a centuries-long misunderstanding.
What, you mean it isn't already?
2. The Shaymin movie is really about Mugen and Zero's relationship. Zero uses Giratina to cover his frustration of being rejected/"betrayed" by Mugen, the one person who made him feel like he belonged and had a place outside of the Reverse World. Mugen feels guilty and helps Ash and Co. to redeem himself for his mistakes. By the end of the film, Mugen and Zero forgive each other and finally consummate their relationship.
3. If I had been in charge of writing the Arceus movie, Damos would've betrayed Arceus on his own volition (rather than handwave it by having him brainwashed by Marcus), only to regret it and sink in sorrow... until Ash and Co. visit him in time to give him a wake-up call, which has him sacrifice himself for the God he truly loved. Alas, that's not what happens in the movie, with or without scandelous God-on-Human romance.
Because the Pokemon Anime writers suck. Thank god I ragequit before the Genesect movie.
4. Pokemon X/Y would actually have a subplot of Professor Sycamore wrangling with a moral dilemma and switching between denial and horror when he realizes his boyfriend is a genocidal maniac.
The Jirachi movie is interesting in this regard, since not only is Diane/Butler a hetship, the dysfunctional and/or tragic romance is actually canon instead of speculation on my part.
Now we just need a dysfunctional and/or tragic yuri couple, and the circle is complete.
You know, it's telling that the healthiest relationship in the above examples is the knight and his clearly-a-Pokemon apprentice. Figures.