I wanted to get this out before any possible update tomorrow. I present my case for Wagstaff being a villain in the DS/T story, and specifically the villain and a big boss encounter (if not the final boss).
Obviously a supervillain
Making the case for Wagstaff being a villain character is not hard. We can start with the writing in his quotes (which is my favorite bit of writing in the Hamlet era of DS singleplayer by the way).
Have you ever sat down and read through Wagstaff's quotes and realized, wow, he's evil isn't he? Just a straight up supervillain? I've selected a few quotes to illustrate this and put them in 3 handy categories:
Totally Normal things for someone to say
Nightmare Amulet = "It uses dark fuel to induce psychic attack! I love it."
Bunnyman = "I much prefer their darker form."
Light Flower = "Is it radioactive? I hope so."
Life Giving Amulet = "Finally a way to experience what death is like!"
Maxwell's Mosquito Trap = "Inspired brutality!"
Gunpowder = "An ingenious invention. Capable of much destruction."
Living Log = "I do wish logs at home were similarly afflicted."
Clockwork Rook = "Such admirable clockwork! I will examine it more closely when I destroy it."
Dessicated Tentacle = "Marvelous! A severed limb!"
Palm Treeguard = "If I could only take such possessed topiaries home with me!"
White Whale = "How rare! I must hunt it!"
Watery Grave = "The deceased won't mind if I raid their graves."
Blunderbuss = "A magnificent killing instrument. Such a sleek design."
Aporkalypse Calendar = "Wonderful! I wonder if I could make the world end sooner."
Unscrupulous Businessman/Repeating mistakes of the past
Snake Oil- "Ah, I made a fortune selling such concoctions in my youth."
Obelisk (inactive) = "I would very much like to introduce this technology to the population back home."
Dark Sword = "Dark fuel forged into a fascinating weapon! Its military applications are endless!"
Piratihatitator (generic)= "If I could return home with this machine, I could revolutionize the world!"
Piratihatitator (burnt) = "My plans for a scientific revolution have gone up in flames."
Queen Malfalfa = "Are you a patron of the sciences by any chance?"
Smelter = "Magnificent! Perhaps I can build a factory here as well."
His Great Purpose/Scientific Revolution
Divining Rod Holder (unlocked) = "Eureka! My destiny awaits!"
Nightmare Throne = "I've found it! The portal that can link worlds! The throne of ultimate power!!"
Nightmare Fuel = "I must find a way to return with this. It will revolutionize the world!!"
Touch Stone = "Another chance to fulfill my destiny!"
Sail Stick = "A superlative utilization of dark fuel. The world will be better for its introduction!"
Pugalisk Wand = "Another vanguard device I could use to bring the world to a new age!"
(Fun little note: The Nightmare Throne and Nightmare Fuel Wagstaff quotes are the only ones of his that ends with double exclamation points!!)
Sure, his quotes show that Wagstaff is clearly good villain material, but we can go further and prove that he is the perfect villain for DS/T. In my opinion a good villain for a specific story has to be a "dark reflection" of the protagonist. My favorite example is Batman and the Joker. This dynamic brings balance to a story and bridges any opposing themes within, such as Science vs Magic in DS. DS already does this with Wilson and Maxwell. They are 2 sides of the same coin, similar in some ways and opposite in others. I can see similar parallels between Wagstaff and Maxwell, Wagstaff and Wilson, and even Wagstaff and Winona. This sets up his potential as a major protagonist almost too well.
Wagstaff is on the very end of the Science spectrum, yet vastly different from Wilson. Wilson is a hobby scientist, and a bad one at that. Before the Constant Wilson was a loner in a shabby house with not much to his name. Conversely, Wagstaff was a successful inventor, businessman, and a master of many scientific disciplines (as shown through many of the observations in his quotes). His perks involve actually building things, as opposed to Wilson whose special power is growing facial hair (although, he does technically have inventions in DST, but they are not exclusive to him/can be made by anyone). Winona builds things, too, but her buildings are themed around helping her friends to survive. Wagstaff makes things that only help himself or destroy things for his benefit.
Compared to Maxwell, Wagstaff is also a person who knows a lot about the Constant. One funny way they're similar is how Wagstaff makes meta observations of the game-like nature of the DS world. Maxwell does this, too, but in a way that seems like he is aware that he's in a game. There is also the dramatic irony in how Wagstaff talks about the Nightmare Fuel versus Maxwell's familiarity with its dangers. Wagstaff sees it as a resource to exploit, which is a major red flag. We know how wrong that can go because of what the game, especially Maxwell, has told us about its history: that the Ancient Civilization overused it to their eventual destruction.
It should also be noted how much work was put into humanizing Maxwell, the villain of the singleplayer game. He had a whole outside-of-the-game story campaign just for explaining his background. Wagstaff has not been given this treatment, and in fact his character works a lot better as the destruction-loving capitalist science man with questionable morals, sans any sympathetic traits. This would make him a stronger final villain as well, even in the wake of Maxwell's stint as the big bad. Wagstaff legitimately is the worst person to have this power, while Maxwell is more of a normal man who got in way over his head. Maxwell also at least seems a little remorseful for his wrongdoings as Nightmare King, especially in regards to Charlie who was innocent collateral damage. Wagstaff doesn't feel like the kind of person to feel bad for any of the hurt he causes, especially since he has "well-intentioned" goals for revolutionizing the world.
If Wagstaff is the villain character I imagine him to be, then there is another mirroring with Maxwell that I think balances out quite nicely:
Maxwell is originally presented as the villain of DS singleplayer, where he is slowly hyped up as the final boss battle of the game, but this is revealed to be a red herring when finding him and releasing him is simple and underwhelming. He then becomes a playable character.
Wagstaff is hyped as a huge character in the lore but is then retroactively added as a default playable character in the singleplayer game, which is underwhelming, but this is later revealed to be a red herring when he shows up in DST as a true final boss fight.
Not Like Other Survivors
Another big reason why Wagstaff is a/the villain of DST is because he cannot work as a playable DST character. This could just be because he was designed as a singleplayer character, and could be changed to work with a multiplayer environment. However, I think there is enough evidence that this likely isn't the case.
Wagstaff's perspective on the Constant is unique from all other characters we've seen so far. He brought himself to the Constant and he sees himself as an explorer of it, not a victim. He was clearly aware of the place before he came there, unlike pretty much everyone. As far as we know, he was not tempted to build a portal the way Wilson was in "Forbidden Knowledge". Since he is so different, I feel like he is specifically built not to mesh with the other characters, which makes his inclusion in the DST cast seem unlikely or at least uncomfortable.
Because he chose to be in the Constant, his motivations run counter to that of all other Survivors. His goal is to not escape and go home, but to essentially colonize the Constant and create a permanent connection to it and the real world. He wants to bring back many things from the Constant, and he wants to exploit its resources, namely the Nightmare Fuel. If he were to join the others in DST, I think they would find his goals too distasteful considering all that they've been through.
Wagstaff frequently expresses a strong desire to communicate with others about the Constant. By the nature of DS singleplayer itself he is never satisfied. Even when he can speak to others, such as some of the Pig Traders, he somehow cannot get them to answer specific things. This is a strong conflict of his character that would be pointless in DST where he can have free access to Maxwell, the Atrium, and now the Ancient Archive. He even says many times that he wants to speak to Maxwell specifically. Being in DST would make things way too easy for him, and for us. That is not good writing.
This may seem like a strange reason, but the fact that he distorts at low HP (which I will refer to as his "projection" due to the "outofworldprojected" tag in his prefab file) is an indication of some sort that he is not a living being like the other characters we can play as. DST is the only time playable characters can become ghosts when they die. This to me feels like a disqualification for being a DST character as well as a very suspicious quirk that can only work in DS singleplayer. If Klei was to bring him to DST they'd have to change this a lot or at the very least explain it in a satisfying way.
Speaking of Wagstaff's "projection", it has to be one of the most intriguing parts of his character. It is the one thing that brings his presence in DS singleplayer in question. What is meant by this projection? Is he really there? If he isn't, then where is the real Wagstaff? Why is he projecting himself like this? Another intriguing aspect of his character is his relationship to the Divining Rod and the Divining Rod base. Wagstaff (or at least his projections) recognize that the radio and the base are his technology, however he does not seem to know why they are there. This is significant because the Rod and the Base are the key and lock behind the Nightmare Throne itself. Whoever built these things is a huge piece of information.
Because of the doubts and questions Wagstaff creates, it feels like his whole presence in DS is a red herring, and his true potential has yet to be reached. A potential, mind you, that was highly anticipated. Wagstaff has been in the lore for a very long time, but only as a name in a 2013 forum post by Kevin Forbes. Being added to DS after so much time was such a cool surprise to us lore obsessed fans. Which is why him dead-ending in the singleplayer game feels... odd. Once he reaches the end of Adventure Mode and finds the Nightmare Throne he rejoices at his success at finding "the throne of ultimate power!!" But once he sits on the throne... nothing special happens. He ends up with the same fate as all the others. It could just be a fitting tragic ending for this man, which is perfectly in line with a game like DS singleplayer. But with all the unanswered questions surrounding Wagstaff and everything he's involved with, it just doesn't sit right with me. There has to be more.
I wanted to end this with a cool big theory about where Wagstaff actually is with lots of detail, but with so little info to go by I only have quick wild hunches. Basically, I think Wagstaff is on the other throne which is on the moon. It ties together this recent moon theming pretty well, and I like the idea of Wagstaff being the White king as opposed to Maxwell and Charlie being the Black king and queen (following the chess theming in DS). I actually came up with this idea before the Forgotten Knowledge update, so I have some hopes that the inactive portal in the Ancient Archive is the portal to this moon throne room. And that "5 guys" teaser image for the next update looks suspiciously like Wagstaff's work, which utilizes what looks like the Celestial Orb (moon magic).
I hope this at least got some of your gears' turning! Thanks for reading.
(Also if I'm right and we see the true Wagstaff again... I hope that he's wearing only one glove.)