The idea of the origins of the Avatar has been kicked around since book 2, but was eventually fitted into book 2 of the sequel series The Legend of Korra.
A false Avatar was planned, which eventually became a major plot point in The Rise of Kyoshi.
During the early planning stages of Justice League, Bruce Timm toyed with the idea of giving the team matching uniforms, but this was quickly vetoed by Paul Levitz. However, he was able to repurpose the uniforms for the Justice Lords in Season 2.
Season 14's "I'm Spelling as Fast as I Can" was going to have a Lead In where Bart realises he wasted his summer and rushes all the activities he intended to do on the last day. It ended up being cut for time and used in "The Monkey Suit" instead, three seasons later.
The Working Title for the season 10 finale, "Thirty Minutes Over Tokyo", was "Fat Man And Little Boy", which later became the title of a season 16 episode.
There were on and off plans to parody The Exorcist in a Treehouse of Horror episode for decades before it happened in season 29's "Treehouse of Horror XXVIII" segment "The Exor-Sis". The first plan was to have Lisa possessed in the opening of season 8's "Treehouse of Horror VII; later, Homer was possessed in a fakeout ending of season 17's "Treehouse of Horror XVI" segment "B.I.: Bartificial Intelligence".
"Hit the Diamond" was going to have a scene where Steven gives nicknames to the Ruby Squad, but it ended up being cut. It took until "Back to the Moon", the Squad's second appearance, for the nickname scene to happen.
The show's fifth and final season had several major plot twist and ideas that had been considered since season one, including Lars' death and revival, Steven entering Pearl's gem, and Steven having his gem separated from his body.
Ruby and Sapphire's wedding was something the crew originally wanted in season four, but network resistance ended up delaying it until season five.
Bob Uecker was going to play a guest role in Teen Titans Go!'s very first season. But because they couldn't find any way to fit him in, he wound up appearing in a season 5 episode instead.
Back when it was planned as the Grand Finale of X-Men: The Animated Series, the "Beyond Good and Evil" arc was supposed to end with recurring characters Bishop, Archangel, Shard and Psylocke being inducted into the X-Men. However, the show was unexpectedly renewed for another season, so this idea was dropped. Bishop would eventually become an official member of the team in the Sequel SeriesX-Men '97.