Toby said/implied more than once that a huge concept of the game is punishing completionist gameplay, IE playing just to get to know all interactions, all items, etc, while forgoing the characters and the universe the game takes place in.
In regards to flowey:
I think that, at the end of a true pacifist run, Asriel/flowey kinda come to terms with the state of his existence, and stop being a omnicidal maniac. All he wants now is to observe how things go. And when you show up again, he'll even try to talk you out of resetting the game, clearly showing some simpathy for everyone else, who all seem pretty happy with what they got. He does, after all, explain that the whole reason he was being a huge psychopath is due to what the fallen human/chara made him experience and the fact that he couldn't feel anything after he lost his soul.
His focus on causing suffering is actualy rather realistic, if you understand how real life psychopaths work. Many studies have shown that, in the end, the entire reason psychopaths end up making people suffer and/or killing people is because they're attempting to feel something, as otherwise they're mostly emotionally dead and get no reaction from anything we view as positive, due to having a natural inclination to such things and/or having suffered some sort of trauma/abuse during their developmental process. This isn't true for all of them, of course.