Serena's crush doesn't matter, it will never progress more than that...a crush.
Greninja's form was retconned into aura bond, lazy writing.
Alain is just another martyr to remind people (other than every single episode he is in) that Leon is the strongest, unbeatable, undeniable, unstoppable and supreme trainer in the world.
I really think the anti-XY theories of Tomiyasu hating XY are still dumb but I can't lie, some of these decisions over these specific characters/plots are suspicious to say the least.