Unseen Academicals/WMG

WMGs for Discworld/Unseen Academicals. Warning: Potential unmarked spoilers.

Lady Margolotta trained Nutt specifically to be a perfect Machiavellian dictator.
Both loved and feared. People (both individuals and as in "a people") love him for who he is, and fear him for what he is (a superintelligent read-the-book-and-find-out). He has potential to be an even better Chessmaster than Vetinari, since people are less predictable than chess pieces and he uses that to his advantage.

Nutt is a heavily altered Big Boss clone.
Like Solid Snake, he's highly intelligent, skilled, multilingual,, and is a rather horrible flirt. Like Liquid, he has serious self-worth issues and unnatural durability. Throwing in a little Otacon DNA could account for the technical prowess and adorkability.

Glenda is a witch.
Possibly without realising it (kinda like Tiffany's grandmother). We don't know if she has any actual magic power, but witchcraft is mostly about having the right sort of personality and intelligence and she does have that. (Also, it makes the idea of her, Nutt and Oats having adventures in Überwald just a little more awesome.)
 * The fact that there are no witches in Ankh-Morpork (at least as far as we can tell) would seem to lend to your theory: witchcraft in Lancre and the surrounding area seems to get passed down from one witch to another, but without any witches to begin with, there wouldn't be anyone to pass it down in Ankh-Morpork. Shame, that.
 * As it turns out, there are witches in Ankh-Morpork, though they keep a high profile - they dress up in so gaudy witch costumes that everybody assumes they're just going to a hen party, or something.

Da Orks came frum da round flat place
The chants (come on if you think you're hard enough, here we go, here we go, here we go), mechanically-skilled orcs who can change size as a reflection of what people think of them, the Waaaagh Shove... Need I say more?
 * The chants and the Shove are both products of Football, and had been around long before Mr. Nutt showed up in Ankh-Morpork.
 * The orcs are stated to have been made from humans, my theory still stands.

Terry Pratchett plays Warhammer
See above.
 * Sir Terry knows about Games Workshop, and even was in talks to write a novel for them (in the early Nineties) but it never went anywhere.

Pepe's problem...
...was not just being gay when he mentions that you have to be tough to grow up poor with his preferences. Given the general nature of the Discworld and the Word of God about him and Madame Sharn, he was the one thing that's worse—a xenophile, with a specific thing for dwarfs.

Nutt will become Vetinari's successor.
As the top of the page mentions, he's got the potential to be an even better Chessmaster. He managed to get the entirety of the football stadium to cheer for him. He can talk people better. He works. And Vetinari likes him. He's the man the city needs.
 * Nutt isn't a people person. He uses big words and brings up complicated concepts. And he's nice, and requires explanations for things everyone else in the city takes for granted. And he doesn't wear a gold suit. He'd be totally wrong for the city if he were in politics. He needs to find his own niche and do good for the city in his own way like a certain Captain does.
 * And it's hinted at at the end of the novel that Ventari plans on making Gilda his personal cook and therfore keeping Nutt close, not to mention giving him something that Margoletta, his rival/love interest (which is really as clear as you can define their relationship) wants as an added bonus, and probably already has plans for him that he's waiting for the right time to activate, so the aforementioned niche is presumably in the works.

Orc speculation
Having  in the same book?
 * Engineered as warriors, nearly impossible to kill, keep showing up after everyone thinks they're wiped off the planet, instinctive push to group action, near-instinctive grasp of mechanical skills he's only read about... There's just no way that's a coincidence.
 * There actually exists a tabletop football game set in the Warhammer universe. Granted, it uses American football...
 * Speaking of, it's easy to see a parallel between Nutt and another member of a race of formerly enslaved super soldiers who is philosophical, well-spoken, well-read, and has a little something inside of him that helps heal injuries.
 * In a similar vein to the above, though this may well be a coincidence, there's an in the Warcraft series who was also

Agnes is with Mightily Oats in Uberwald

 * Glenda is in many ways just like Agnes. There's speculation that she's a witch (see above, that wasn't this troper). She has an inner Glenda reminiscent of Perdita X Dream (though to be fair, it's also sorta like second thoughts are described in the Tiffany Aching books). She's also pleasantly plump, so to speak, and slightly self conscious about it (though she gets over that). Now Glenda is in love with  and he's stated to be going to take Mightily Oat's place in Uberwald. Agnes and Mightily had some romantic interest near the end of Carpe Jugulum. So Glenda and   would be taking over for Agnes and Mightily. It would also explain why Agnes has disappeared off the face of the earth during the Tiffany Aching books.
 * Oh great, so now we have Nitt and Nutt together? All that's missing is Nutter from Good Omens. I sense a Dumb & Dumber spoof coming up...

Nutt will turn the orcs into a football team
After he goes out and civilizes the other orcs he'll bring them back to Ankh-Morpork and use their teamwork instincts to make them into an all-orc football team, because that would be awesome

This is the book where Vetinari won
Just what does Vetinari want? In this book we learn his second goal, in addition to making Ankh-Morpork work, "to prove the moral superior of the supreme being." Since the early days of when Discworld was becoming what it is now, Vetinari had been slowly but inexorably drawing together first the various human factions, then drawing in Dwarfs, then Trolle, Werewolves, Vampires, Nobby Nobbs, Gorgons, letting them all in, giving them ALL a chance. In this book he manipulates the Shove into conquering itself and gets Ankh-Morpork to think "hey them Orcs aren't so bad after all." Most telling of all, he has cultivated a city alone on the Disc where citizens will break into his palace to warn him. Granted, he's Vetinari so he already knew, but since his successor will not be him (this being the very point of a successor), he has given the next man or woman for the job the gift of a populace who gives a damn.