In the opening, Pinocchio rejects Rumpelstiltskin's offer to make him a real boy with the observation that nobody wants his kind of deals any more. This all but explicitly brings up the other reason Rumple wants Shrek gone; Shrek's example encouraged people to be comfortable with who they are rather than seeking new ways out of their lives, making it basically impossible for Rumpel to make his old deals as people are more willing to find happiness by themselves.
Rumpelstiltskin pays the Pied Piper in advance. Which makes sense given that the mayor of Hamelin stiffed him and suffered the consequences.
When Pinocchio turns Gepetto disguised as Shrek to Rumpelstiltskin, he obviously doesn't fall for it. Pinocchio insists it's Shrek, making his nose grow. But his nose doesn't grow when he says "these ogres are crafty." Which is technically true, since there's a resistance of ogres in this world.
Rumple says "Sign the kingdom over to me and all your problems will disappear" and Harold and Lillian vanish, obviously removing their problems. This makes more sense than you think. Obviously the only problem they're thinking of is their Princess problem and yeah, that vanishes, and yeah, Rumple probably didn't need to wipe them out to fix it, but their problems don't end there - there's the detail of Shrek showing up, then the king gets sick and the kingdom needs a new king - whom originally Shrek went and fetched - and of course there's all the little problems that a king and queen have to deal with. Rumple wasn't wiping them out for the sheer joy of it - it was the ONLY way he could possibly remove ALL their problems. Even if he wasn't so bad, he couldn't have kept the magical contract WITHOUT wiping their existence and taking over the kingdom. That's magic for you. He knew that. They didn't.
The area around Rumpelstiltskin's palace is a desiccated-looking wasteland despite Far Far Away never being implied to have such a climate. Of course it is when he's seemingly created a ruling class of witches who dissolve on contact with water. That's probably their native climate!
Why do we never see Fairy Godmother and Prince Charming in the movie? Equivalent Exchange. Remember, Harold knew of the plan to marry off Charming to Fiona and forced into it by his own warty problem; it was another problem that Harold himself wanted to get rid of, and Rumpelstiltskin's magic would require a life to get rid of a life (two in fact) for his magic to work. The kingdom was probably just a bonus to the contract.
Puss in Boots being turned into Fiona's spoiled, fat pet is probably deliberate on Fiona's part. Remember in Shrek 2 that Puss was the only assassin willing to go up against an ogre. Fiona probably found it easier to turn her would-be assassin into a beloved pet.
This counts as Fridge-Heartwarming when one realizes this is basically what Shrek did with him as well when they first met: turn him into an animal companion. Even in a timeline where Fiona has become an embittered version of herself, she and Shrek do think alike.
Rumple ends up imprisoned at the end of the movie and is still confirmed to be that way in Donkey's Christmas Shrektacular. This isn't just Laser-Guided Karma; Shrek and friends are being practical. Had they simply banished Rumple or if he escaped, he could get far away where presumably nobody knew of his reputation and started more trouble with his magical contracts, probably even altering history just as he did before!
Why does the Big Bad Wolf accidentally pop the balloons he blows up during the party? Because he is the Big Bad Wolf! The one who will huff and puff and blow your house in!
With the added context brought by Puss in Boots: The Last Wish about Puss' 9 lives, Puss becoming an overweight housecat to Fiona is exactly what he did with Mama Luna. His 7th death (burned to a crisp when baking with Gingy) happened in Far Far Away after meeting Shrek. It's entirely possible that in the alternate timeline, Puss died twice because of Rumple's Crapsack World and met the Wolf earlier that in the original.
Adding onto that, he may have met Fiona because of a previous failed assassination attempt on her (considering he's willing to go against an ogre). After meeting the Wolf, Puss may have "convinced" her to keep him as a pet the same way he did with Shrek.
Rumplestilskin's character parallels the other main antagonists from the other movies; He is short-structured and desires power like Lord Farquaad, he uses magic to not only help people but to benefit for his own personal gain like the Fairy Godmother, and just like Prince Charming, his motive was ignited when his intentional plans failed when Shrek rescued Fiona from the Dragon's Keep.
Comparing the height and width of the storybooks of both Shrek and Puss in Boots on Shrek's shelf at the very end, it kinda represents the aspects of the respective stories, with Shrek's tale being bigger in story and containing more chapters, in reference to the amount of movies in the main Shrek series, while Puss' book is smaller in both story and chapters, representing the Puss in Boots spin-off's status as a duology.
In Forever After's alternate universe, Donkey says that he needs his job pulling the witches' carriage because he doesn't want to go back to Old McDonald. Considering his ragged appearance and the way the witches whip him when they want him to sing different songs, just how bad must his old job have been?
If Fiona says she rescued herself by escaping the Dragon's Keep, then Charming presumably never made it to her. He's never mentioned by anyone, so it's presumable that he was killed by Dragon, as were any knights sent by Farquuad.
And that's the best case scenario. It's just as likely he returned to Far Far Away empty-handed, only for both him and Fairy Godmother to be captured by Rumpelstiltskin's witches and subsequently executed-and for good reason. Stlits wouldn't want anyone around who has a personal interest in challenging his rule, and especially not if those someones have magic rivaling that of his own forces.
In Forever After it is implied that only one timeline can exist at a time- the original timeline is replaced by the alternate timeline, and then replaced again by the original timeline when Rumple's deal is broken. When this happens all of the alternate timeline characters are "poofed" out of existence as their reality crumbles. They are then replaced by their original counterparts- yet Shrek is the only one who retains any memories of the alternate reality note though an argument could be made that Rumpelstiltskin also has memories of the alternate reality. This means that the original timeline characters and alternate reality characters were separate beings. And all of the alternate timeline characters' existences were erased completely. Alternate Fiona never got to experience having children with Shrek or living in a tyranny-free world because she disappeared from existence 10 seconds later.
