For one, there's Lysandre. After Lysandre made a giant hole in Geosenge, Sycamore's all "oh noes, I should have stopped him. I knew he was crazy about keeping things fabulous, but I should have stopped him, my fault, etc". And after that incident, the prof doesn't mention anything about his colleague anymore. Nobody even bothers to try and remove the rubble from the crater to see the aftermath of the blast (hey, if there are Pokemon that have a sense of smell 1 million times greater than that ofa human, it shouldn't be too hard to remove boulders from a 50-100m deep pit, now would it?). The only time someone alludes to his fate is when your main rival gives you the Absolite while saying something along the lines of "oh I have 2 Absolites, you can have one. Gotta show Lysandre we aren't politicians!"
Next is AZ. The ancient king of Kalos only shows up 4 times in the game.
1. When you finished kicking Team Flare out of the power plant.
2. When you find him locked up in Lysandre Labs.
3. After you escape the Lysandre's self-destruct attack.
4. At the parade where he finally reunites with Floette.
After that, nothing. We don't get to battle him again and we don't get to know what happened after the ceremony. He's just gone. Daferk GF. Give us an epilogue or a side quest for the poor guy! I wanted more information about the ancient war, AZ's immortality, what he did during 3000 years ago - present, and AZ himself instead of just:
"War happened, king's favourite 'mon died, king built machine to resurrect 'mon, used machine to kill cuz he was angry, 'mon left cuz king turned evil, king wandered for 3k years to find friend".
In fact, all of the ancient plot presented in the game revolved around the ultimate weapon...
And lastly, the gym leaders. Aside from Korrina, Wulfric, and maybe Clemont, the gym leaders were given a rather one dimensional personality and a purpose that consisted of giving you their badge and a TM.