The protagonist has Asperger's Syndrome.The player character is an expy of the Pokemon franchise creator, so why not?
The protagonist in Super is the same one from GtI
- Following the WMG above that protagonist in GtI doesn't return and they don't have amnesia. They might prefer to stay in human world. The protagonist only return to save the world again, but they get amnesia this time.
- Hydregion seems to be familiar with you.
The Bittercold and Dark Matter are the same/similar beings.
- Both of them are said to be made of the negative emotions in Pokémon's hearts, but there are a number of differences, such as appearance, and abilities. Here's this troper's theory on the differences; The Bittercold came about because Kyurem tried to accelerate Dark Matter's forming process in an attempt to get the wait over with. The end result is that Dark Matter was "stillborn", left half-formed, and so it wasn't sentient. Despite this, it still had it's mind control powers, but it used them purely on instinct, to disable anything it saw as a threat; hence the Winds of Despair. If we take a look at the cores of the Bittercold◊ and Dark Matter◊, you can see that they look almost exactly the same. So, the Bittercold is what you get when you try to wake Dark Matter up early.
It's unlikely Dark Matter is really, truly dead.
- You can't kill the embodiment of evil that easily, after all. Likely it was only this current configuration, the mind and consciousness currently held by the amalgam of the darkness all hearts and souls, that was obliterated by the Partner's acceptance of it. However, the essence of the entity is likely to re-manifest whenever the evil residing in Pokemon's hearts and souls surges again. Building on above WM Gs suggesting the Bittercold and Dark Matter are possibly different incarnations of the same being, whenever it returns it may look, act and think differently but it's still the same thing returned from the Void (hopefully we won't be dealing with Exdeath any time soon!). Like suggested before, the Bittercold would have displayed the essence of evil and negativity beginning to coalesce into a 'living' form, but fought early enough in its development to stop it from gaining true thought and conscious willpower; as shown in Super, allowing that thing to self-actualize would make it WILLINGLY malevolent rather than instinctively if its current incarnation is allowed to progress too far. It would take either purging all sentient life of darkness and malevolence (which would be bad news for the concept of free will) or convincing ALL sentient beings to accept the existence of evil, at least in the Mystery Dungeon universe(s) if not the whole Pokemon multiverse, to finally get rid of it for good. It's hard to subvert As Long as There is Evil, sadly. Perhaps this is also why their designs seem eldritch in a...simplistic way, as though certainly intricate they were overall basic geometrical shapes, rather than anything recognizable as a true "living" entity, and perhaps if and (likely) when it does return it may well have progressed farther in the development of its new incarnation, becoming a greater threat than ever before.
The player and partner's relationship was originally intended to be more than platonic.As shown under the Ship Tease trope under the main page, there's a lot of sub-text between the player and partner. While the series has been no stranger to this in the past, what with the whole baby Manaphy of T/D/S, notably, the player is never referred to by gender pronouns throughout the game. Similarly, the in the versions of the game where he is referred to by gender pronouns, he's always male, while the partner is always female. As such, there's a lot of evidence that seems to suggest that the relationship between the player and partner was going to be more than platonic friends at some point in development. Why was it changed? Possibly because of, even with the Ambiguous Gender protagonist, it still could possibly become awkward at points throughout the story if they're based on the player. Similarly, there could be the rather unflattering bestiality undertones that Nintendo likely didn't want to deal with should it stir a controversy.