Flip-Flop of God: Jason Fry revealed on his Tumblr blog that while writing Servants of the Empire, he was told by the Lucasfilm Story Group to use terms like 'stone' instead of 'duracrete' (as Legends was fond of Calling A Rabbit A Smeerp for almost everything), due to how confusing and distracting it could be to readers. However, other books do use terms like 'duracrete'. Though it is worth noting that said other books are aimed at older audiences while Servants of the Empire was aimed at a younger audience, so it could just be for their sake instead.
I Knew It!: Almost immediately after Lucasfilm announced that the old Expanded Universe had been Exiled from Continuity and rebranded as Star Wars Legends, fans of Ensemble Darkhorse Grand Admiral Thrawn started insisting that Thrawn would show up in the new Expanded Universe eventually. They were absolutely adamant that he was still around, even though Timothy Zahn's The Thrawn Trilogy—where he was introduced, and later Killed Off for Real—had officially never happened. But in 2016, it turned out that they were right after all: it was announced that Thrawn would appear in Season 3 of Star Wars Rebels, and that Zahn would be penning the new novel Star Wars: Thrawn, which would officially reintroduce everyone's favorite Chiss in White with a new canon backstory.
Rebels is quite fond of reusing old concepts, such as the Bendu (the original name of the Jedi was the Jedi-Bendu; Yoda was also originally going to be a gigantic creature, which is what Bendu is), Ashla and Bogan (the original names of the Light and Dark sides (also reused in Legends' Dawn of the Jedi), character and place designs, and so on.
They also reuse concepts from more recent times too such as The Force Awakens, like the Fifth Brother's design being based off of an unused Knight of Ren design and Ketsu's helmet being one of Kylo Ren's concept art helmets.
The show's focus on a crew is based off the original concept of The Clone Wars, where a Jedi master-apprentice duo would be traveling with a smuggling crew during the war.
Saw Gerrera was originally supposed to be in a live-action show (presumably Underworld). After the Disney buyout, an extremist character was needed for Rogue One, leading to Saw's original purpose being refitted.
According to Pablo Hidalgo on Twitter, a bunch of parts about the new lightsaber lore including the bleeding crystals were actually started way back during the production of the youngling arc from The Clone Wars. There's also a rumor that the crystal bleeding was originally going to be used in Revenge of the Sith, though Hidalgo can't confirm or deny it as he was only introduced to the idea during the making of The Clone Wars.
What Could Have Been: One of the most famous is the proposed mid-nineties novel Alien Exodus. This was intended to reveal the origin of humans in the Star Wars universe, with a group of astronauts (one of them implied to be descended from Curtis Henderson of American Graffiti) escaping a computer-dominated future Earth (supposedly the same as the one featured in THX 1138) and somehow ending up "a long time ago in a galaxy far, far away".