Yeah, it's a solid theory.
Season finale was good, but the evil Morty episode should have definitely been the last one. It would have been a great ass pull if they had played up the fact that they were going to Atlantis, shot a few fake promo scenes, made it look like a massive season finale, and then all of a sudden it's just an episode about the citadel. It would have been good.
Just move this episode with the president to one down in the list and it would work. It would make a little less sense in terms of narrative (Morty being super cool with Rick at the beginning of going to Atlantis, but then being not cool with him after the actual season finale), but it would work out in the end.
If I download the seasons, I'm gonna just move the episodes around my self. New order and all that.