Sometimes it's clear who in a story will be the Chosen One—the character who gets to wield some awesome power or save the world from certain destruction. But sometimes destiny cheats or gets sidetracked along the way.
Here are character who were alternative candidates of prophesies, had their birthrights taken Jacob-and-Esau-style, or just didn't make it to their fated destinies. These aren't the folks who turned their nose up at their heroic or villainous fates. (There are enough of those to populate many more lists.) Add your favorite almost-Chosen Ones in the comments!
Neville Longbottom (Harry Potter): Neville is the classic example of a guy who was very nearly the Chosen One—to the extent that many readers suspected that he might be the true subject of Sybill Trelawney's prophecy. Ultimately, there were two boys who could have fulfilled the prophecy and defeated Voldemort: Neville and Harry Potter. In the end, the ultimate Chosen One had to be selected by Voldemort himself (marked as his equal), and he chose Harry, whose half-blood lineage reminded Voldemort of his own.
Grandpa Max (Ben 10): When the alien Xylene sent the powerful Omnitrix to Earth, she meant for it to reach Max Tennyson, not his grandson Ben. When Ben receives the Omnitrix, however, Max proves an invaluable mentor thanks to his familiarity with extraterrestrial weirdness. It's also not the first time Max missed out on a life-altering event; he was originally supposed to be the first man on the moon, but left NASA before lunar mission launched.
Spike (Angel): Spike and Angel have a rivalry that has spanned lifetimes, and after Spike became ensouled and a Champion of the Powers That Be, that rivalry included the Shanshu Prophecy. After all, Spike was a vampire with a soul; he'd been willing to sacrifice his life as a Champion; why shouldn't he be the subject of the Shanshu Prophecy? And when Angel signs away his rights to the Shanshu, it seems that Spike is the only candidate left to fulfill the prophecy. But Angel's destiny is saved by Wolfram & Hart's failure to file the contract Angel signed, and eventually Spike realizes that he has to find his own destiny instead of glomming onto Angel's. It hasn't been fulfilled yet, but it turns out that Shanshu Prophecy may not be all it's cracked up to be anyway.
Charles Xavier (X-Men): The mutant telepath was actually Cyttorak's first choice to become his avatar—the being known as the Juggernaut. But it was Charles' stepbrother, Cain Marko, who got his mitts on the Crimson Gem of Cyttorak. On the one hand, Cain may have been a better fit for Cyttorak. On the other, Charles becomes the Juggernaut in a 1990 What If? story and proved a pretty power-hungry figure.
Rhaego (A Song of Ice and Fire): Unlike most of the characters on this list, Rhaego didn't lose his Chosen One status to a rival; he lost it because he was never born in the first place. If he had been born, Daenerys and Khal Drogo's child would have been the fabled Stallion Who Mounts the World—the most powerful khal ever to live. But Daenerys traded the life of her unborn child for a dubious spell from Mirri Maz Duur, a desperate, if ill-advised attempt to save Drogo's life. There are, however, other potential messianic figures wandering about the Game of Thrones world, and perhaps one will prove to be Azor Ahai reborn.
Jake Talley (Supernatural): Why put all your eggs in one Chosen One's basket when you can make yourself a whole mess of Chosen Ones? The yellow-eyed demon Azazel cooks himself a bunch of Special Children, each infused with demon's blood and carrying the potential to lead an army of demons in the war against humanity. Then he gathers them all up and has them fight to the death until only one Special Child is left standing. That Special Child is Jake Talley—at least until Dean has Sam resurrected and Sam kills Jake in return. All's fair in destiny and war.
Harth Fray (Fray): In the history of the Buffyverse, all Slayers and potential Slayers are female, but Harth Fray, twin brother of the Slayer Melaka Fray, got the Slayer psychic powers. It may well be that Harth was just one chromosome away from being a potential Slayer. Of course, being a Slayer's sister doesn't guarantee that you'll be a potential, (Dawn wasn't one, and she was made from Buffy) but Harth makes a good case for being just the wrong side of Chosen. In the end, the local vampires decide he's their One anyway.
Riku (Kingdom Hearts): In the Kingdom Hearts games, Terra actually does select Riku as the inheritor of his Keyblade, but when you grow up on a place called Destiny Island, fate isn't always so straightforward. Riku opens the door in the Secret Place, and disappears into darkness just before the Keyblade appears on the island, making Riku's friend Sora its wielder. If Riku had stayed on the island just a little longer, the Keyblade would have been his. However, the Keyblade does have some residual attachment to Riku, and he is able to wield it himself.
Turbo Thunder (Fairly Oddparents: Wishology): A denizen of Wonder World, Turbo Thunder was prophesied as the great hero who would defeat the Darkness. But when the Darkness attacked Wonder World, Turbo slept through the entire thing, and his destiny passed to young Timmy Turner.
Brian (Life of Brian): There was never a chance that Brian was going to be the Christian Messiah, but he was born literally steps away from the manger where Jesus was born. Despite not being the film's actual son of God, Brian is frequently mistaken for Messiah, and has some truly extraordinary adventures, including a brief ride in a UFO. Unfortunately, it turns out just as badly for him in the end as it does for Jesus.