Please Note: While much of the information in this piece is, by now, common knowledge, certain key elements became known initially through the efforts of specific journalists. Wherever possible, those sources have been cited and linked. Also Note: It should go without saying that a spoiler warning is in effect.
Peter Parker, Costume Thief
For my money, it's a mark in Spider-Man's favor that it doesn't sweat the small stuff of superhero mechanics. Peter Parker transitions from his chintzy home-made "Human Spider" getup to the ultra-sleek, meticulously-manufactured Spider-Man spandex with no explanation whatsoever. But in an early draft of the screenplay by writer David Koepp, that wasn't the case.
In this version - written back when Doctor Octopus and Green Goblin were both supposed to be in the first movie - Spidey wears "not quite there yet" versions of the suit throughout the film, alongside a running gag about unlicensed Spider-Man merchandise actually looking better than the real thing. At the film's climax, when Peter finds himself needing to rush off to the final battle with no suit on hand, he solves the problem by ducking into a Halloween Store and borrowing - at last - the "proper" Spider-Man costume.
Hell Hath No (Shorter-Lived) Fury
X-Men: The Last Stand ties its already terrible story into even bigger knots with a drive to kill off or "de-power" various characters who, coincidentally, were played mainly by actors whose contracts were up for renegotiation (read: might suddenly cost more.) One of the biggest write-offs was Rebecca Romijn's Mystique, who gets dumped by Magneto after she's unwillingly cured of her mutation and sells him out to the feds in retaliation.
In the movie as-filmmed, it plays out like a blatant example of "kick the dog" to make sure the audience still knows Magneto is bad even though the film is haphazardly stumbling through one of the biggest "Magneto kinda has a point" stories in X-Men history - not for nothing can you now buy "gay pride" t-shirts emblazoned with rainbow-colored Magneto quotations from this movie. Thing is, it wasn't supposed to be.
Originally, Mystique was supposed to turn up at Magneto's side for the film's climactic "A-ha! Maybe we're not totally cured after all!" final stinger, but Romijn's scheduling prevented her from being able to film the scene.
John Connor Is a Fake and Skynet is Misunderstood
Terminator: Salvation has a strange dynamic going on: John Connor (Christian Bale) doesn't seem to be all that good at the "savior of humanity" role he and others believed he's been destined for. Instead, Sam Worthington's Marcus Wright - a 20th-Century death row inmate resurrected as a half-human/half-Terminator cyborg - seems to be the more "classical" hero, a born leader and hyper-capable soldier. After the big final battle in Skynet City, Marcus ultimately sacrifices himself to give Connor a heart transplant; leaving audiences to wonder why we spent so much of the movie following some guy who dies and when Connor was going to turn into the Mad-Max-meets-Oscar-Schindler badass we've been hearing about for three movies.
Well, originally Salvation's big gamble was to pull a huge twist that would've changed everything about the Terminator mythology. Believe it or not, when Marcus snuck into Skynet City (he was supposed to be the main character while Connor was going to be a mysterious character who we never saw until the very end), he wasn't just supposed to find the usual chaotic factory Terminator movies have to end in. He was also supposed to find - I kid you not - a beautiful seaside resort town. Full of humans. Really. Turns out, all this time Skynet has actually been trying to prevent human extinction by keeping a few oblivious "choice" people alive and pampered in this resort while wiping out the "stragglers" in The Resistance. The Terminators have been - in their own way - trying to save us, and the big Final Battle would've been humans versus Terminators in an artificially-recreated Club Med. And that's not all.