Screwed by the Lawyers: Whilst the event is billed as featuring every Spider-Man ever, there are eight that Marvel are unable to use due to rights issues. Whilst one remains unconfirmed, it has been confirmed that the Sony Spider-Men (Tobey Maguire, Andrew Garfield, The Spectacular Spider-Man, and Spider-Man: The New Animated Series) and the Amalgam Universe Spider-Men (Spider-Boy, Spider Clone, Spider-Boy 2099) can't appear. However, the crossover event does get around some of this by having the versions from the live-action films by Sony referenced in Spider-Verse #2 by mentioning Spider-Men that resembled Tobey Maquire and Andrew Garfield when unmasked, albeit not by using the actors' names.
The story was originally designed as featuring the Superior Spider-Man as the lead. It was almost ready to go in print, when the entire Marvel creative summit suddenly realized the implications of it being SpOck and not Peter's story. The entire room then agreed that a storyline featuring every Spider-Man ever should star the original as the main character.
Because of that, SP//dr and Silk weren't originally supposed to play a role in the event at all, with Silk's debut being part of the Original Sin storyline, set after Peter already got his life back.
Spider-Men was originally going to be something of a Prologue to this event, with Bendis and Slott being co-writers, but Slott, realizing that Bendis wanted to make it a more personal story, opted out and instead requested that he'd get use Miles for his story instead.
Spider-Gwen nearly didn't exist. The original idea was that there was supposed to be an Uncle Ben who was bitten, but the writers decided to hold him back for a later point in the story.
Spider-Gwen as a character was also going to be entirely different, what Slott describes as a more "boring" interpretation. Likely closer to her 616 counterpart. Slott credits Jason Latour and Robbi Rodriguez for redesigning both her look and personality until what it currently is, for the better.
On a similar note, Spider-Punk wasn't even in the script at all. Artist Olivier Coipel interpreted Spider-UK as having a punk look instead of a Union Jack costume. In this case, the design was so good that another Spider was created specifically for it.
Spider-Ham was supposed to be stuck on Earth-616 at the end of the event and have occasional adventures ala Howard the Duck. But the revival of Howard's solo series in the aftermath of the Guardians of the Galaxy made Spider-Ham's presence redundant.
While Kaine's death was never meant to stick, the original plan was to let him lay low for a while and reveal his survival/rebirth in a flashback later. However, Dan Slott predicted the fan backlash that would follow and made sure to let people know Kaine wasn't really dead.
The talking Spider-Mobile briefly appearing in The Amazing Spider-Man Vol. 3 #12 was supposed to have a civilian identity of Peter Parked Car.
Dan Slott has stated he does not consider the Marvel Handbooks to be canon and is for the most part completely disregarding them when it comes to the universe designations not named in-comic. The Marvel Comics Database wiki has in turn chosen to disregard this statement due to essentially being a fan-made online version of said Handbooks, and lists the retconned designations as alternate versions instead.