Lack of Agency

It seems like my character doesn’t do much. The Abyssal leader says “even if you win, I’ll still do what I want” but why does my character let her? I just knocked out her lugia. How can the lugia still flood the planet? It’s fainted! And later the guy with Kyurem and Zekrom knocked Orians Reshiram unconscious, goes “to the victor go the spoils” and took his reshiram. Then when I beat him he just walks away? Why didn’t I give the dude his reshiram back? If he can do it, why can’t I? Seems like the battles are completely pointless in this game. The bad guys just do what they want until some other character breaks their magic rock and stops them or whatever. Just feels bad man.