I just finished my "second" run of this game, cause I ran into issues the first run, and I got softlocked out of my shaymin encounter after the end boss. The tree won't get removed, and I'm pretty sure I softlocked myself out of the Cresselia encounter, too. I'm not sure if there's fixes, which I hope will be in the near future, but other than those minor inconveniences I'd say the game is very well made and the story is enjoyable