Update: I just caught one of the Trio. The issue was that somehow, someway, I had encountered Dialga and Arceus from other quests (I don't even know for sure) without getting the prerequisite items. However, I also had started Garchompite quest, so Rowan was stuck on telling me the riddle to solve in front of Cynthia, in order to battle her. So he wasn't able to tell me about the items. I finished the Garchompite quest, Rowan got unstuck, and found the other 2 orbs, battled Palkia Dialga Arceus and proceeded from there. Somehow I had already completed the requirements with Starly Bidoof and Magikarp for the ghost guardians, which should not be possible given that the quest was stuck. Anyway, what's done is done, I got my legendary. And oddly, I got a Dread Plate sitting in my bag while the other 2 items disappeared. I guess it's some kind of souvenir xD
@Epithet Could you please close this thread? Also, if you want you can notify the team about this weird incident so they have the info for any similar cases.
Cheers!