Why is everyone mad that Lillie is the main character and not the main character? This is a clever tactic by GameFreak that shows their desire to stretch out the universe and deviate from the standard formula.
To prove my point, look no further than Game of Thrones. In the series, the main character is Tyrion Lannister. (If you refute this point I would advise you to google all the proof that shows that Tyrion is in fact the main character in GoT). Tyrion is not the chosen one or even the hero of the series. Hell, he's just a midget. Jon Snow is the hero of the series—but he's not the main character. In other words, shows with more advanced and fleshed out storylines use the same tactic that GameFreak is deploying. This leads me to believe that GameFreak is trying to advance beyond the same work-out formula of having the main character be the chosen one. If you don't like it, you clearly aren't paying attention.