Live Another Day has Cheng Zhi as the main antagonist. Although fans were expecting some familiar faces to show up other than Jack, Chloe, Audrey, and James Heller, he was genuinely the last person anyone was expecting to see.
Similarly, Season 8 brought backCharles Logan to fill the role of Big Bad, despite him having no involvement at all with the conflicts going on during the first half of the season, being on the way to pulling a HeelFace Turn during his last appearance, and being last seen in a state of Uncertain Doom.
Milo Pressman was a minor tech guy working at CTU during the first season who disappeared without explanation. In Season 6, he returned from his Long Bus Trip to become a main character for the season, long after most fans had forgotten about him entirely.
Though it was announced beforehand, those familiar with canon were probably surprised that Non would appear as a major villain, sans his usual boss Zod. (And this is before he's reduced to Dumb Muscle.)
Legends of Tomorrow: No one expected the Reverse-Flash to be running from something... namely, the Black Flash, the abomination that used to be Zoom before the Time Wraiths got to him.
One in particular was shocking enough to get some major discussion after the fact (as the secret was kept until it showed on TV) was the Snyderverse version of the Flash. In other words, the Arrowverse is connected to the DCEU.
In season 5 of Angel, Giles sent a member of the Scooby Gang to help Angel. Buffy? Willow? Xander? Faith? Dawn? Nope. Andrew. This is justified however, as Andrew explained that the group didnt want to work with Angel anymore after his decision to join Wolfram & Hart, meaning that it would make sense for them to send one of their least useful members who also didnt have a history with Angel.
Who ends up being the final Big Bad of Buffy the Vampire Slayer? The First Evil, a Monster of the Week who tormented Angel in one episode of Season 3 and then never appeared again once during all of that time between seasons 3 and 7. No one could have predicted such a minor character would get such a big role.
Da Vinci's Demons has the titular character meeting none other than Vlad the Impaler (a.k.a. Dracula).
The Master is a frequent subject of this, appearing halfway through to turn out to be The Man Behind the Man of one alien scheme after another. During Anthony Ainley's tenure, the production team sometimes went so far as to conceal his presence in a story by using his current alias as the character name and turning his actor's name into an anagram. This was deliberately inverted in "Frontier in Space", however, when the Master turned out to be working for the Daleks.
Davros does this all the damn time; it might as well be his defining character trait.
In "The Invasion of Time", no one was expecting the Sontarans, of all races, to be the masterminds behind the plot.
Omega turning out to be The Man Behind the Man in "Arc of Infinity" is unexpected not only from a character standpoint, but from the show's perspective as he hadn't appeared or been mentioned for ten years.
And in "The Day of the Doctor", it wasn't much of a surprise when all the past Doctors show up... but when Twelve makes an appearance, a month before the Christmas special where he was supposed to debut, that turned quite a few heads. On top of that, Tom Baker makes a surprise appearance at the end as the Curator.
The production team can pull this off all the time these days by not listing important characters and actors on prereleased cast lists and only crediting them in the episode itself.
For Series 10, it's John Simm's Master, who hadn't been seen in seven years and was in no way expected to return. Especially given the implications: there's never been a multi-Master story before. It would have been even more unexpected, however, had the BBC publicity department not interfered by announcing his appearance early (although this was to head off the tabloid newspaper The Sun, which was about to leak the story).
Also from Series 10 is Nardole. First appearing as a bumbling Comic Relief character in "The Husbands of River Song", the thought he would become one of the Doctor's companions never crossed anyone's mind; especially since all promotion of companions for this series was given to Bill with no hint up until his reveal there was a second one.
Series 12 premiere "Spyfall" kicks things off with a cliffhanger involving the return of the Master. While pre-publicity had revealed that recurring antagonists the Judoon and Cybermen would be back for the season, absolutely nothing hinted at the Master, especially since series 11 had gone out of its way to avoid using old enemies. No one even knew that the actor cast in the role would be on the show, let alone who he was playing.
Davros again, at the very end of the Divergent arc.
Vinnie Jones once guest starred on Elementary as a character known simply as "M". He's strongly implied to be Sherlock's longtime nemesis Moriarty. He actually turns out to be Sebastian Moran, another character from the Sherlock Holmes mythology.
It seems pretty safe to say that The Gifted isn't a show that focuses on "expected characters", so this could apply to anyone going forward.
Beautiful Dreamer, renamed Dreamer, is a highly obscure character, debuting in Power Pack of all things. No one expected her to be in this series.
Despite being an evil mutant hunter, no one expected Ahab considering he is closely associated with Rachel Summers and the contemporary setting of the show.
Shatter, a very minor character whose most significance was being a victim of a Sentinel attack and losing his powers in the wake of M-Day, is also an unexpected addition.
The Strucker family as a whole, due to the rights of Wolfgang Von Strucker clearly being with Marvel Studios, Andrea and Andreas Von Strucker are mutants whose rights lies with Fox. The X-gene being inherited means their children, grandchildren, and great-grandchildren all are potential mutants.
The Season 1 finale features a cameo from Evangeline Whedon, complete with a tease of her dragon form.
Kamen Rider Gaim has a completely standalone villain for its final episode. It is indeed someone from the past, but it being Kougane, the Big Bad of the summer movie, came right out of nowhere.
The Mandalorian's debut episode shocked the Star Wars fandom when the bounty target was revealed to be a fellow member of Yoda's species, and a baby at that. This is significant as the franchise shied away on expanding the lore related to Yoda or his species.
Season 2 threw a few more surprises along the way, with the live-action debut of fan favorite Ahsoka Tano, a still alive Boba Fett, and Luke Skywalker, looking exactly like he did in Return of the Jedi!
At the end of series 4, Tristan and Isolde were introduced. It felt a little random considering a) they bore no resemblance whatsoever to their legendary counterparts, b) they didn't actually contribute much to the plot, and c) they disappeared entirely after their two episode appearance (Isolde being Killed Off for Real and Tristan disappearing without explanation).
The Grand Finale saw the return of Balinor, Merlin's father who hadn't been seen since the end of season two (and had been killed off in the same episode he was introduced).
In season three a character calling himself Taliesin has a minor role; an odd inclusion given that the legendary/historical Taliesin is only tangentially related to Arthurian legend.
Mystery Science Theater 3000 shocked people when Dr. Larry Erdhart, Dr. Forrester's original sidekick from the KTMA era and the first season of the cable run, reappeared.
Episode 9 begins with a cameo appearance of Doctor K, who helps the team to figure out a way to save Mayor Daniels.
Episode 10 and 11 was another Metal Hero crossover adaptation as we get the American version Space Sheriff GavanType-G as Captain Chakku.
Everyone knew they were going to adapt the three dinosaur Ranger teamup from the Go-Busters vs. Kyoryuger. No one expected the lead-up to not only give us a proper Beast Morphers/Dino Charge team up, but also bring back Keeper and Sledge!
You think we'd get a breather after that, right? NOPE. Suddenly, we find out that Evox is more than just some snake-like virus. He's actually the Venjix Virus resurrected, finally completing a Sequel Hook nearly ten years old!
Pretty Guardian Sailor Moon: Ami's mother and Rei's father. In the manga, each only appeared once long after the end of the Dark Kingdom arc, making their appearances in this series a little unexpected.
The second season of Sense8 had hacker Nomi Marks reach out to help from someone known only as "the Guy". In a clandestine meeting at the cinema, it turns out to be none other than Anonymous, appearing in his familiar Guy Fawkes mask. It's safe to say no one saw that coming!
Some of the Injustice League. Parasite is a long-time enemy, Livewire is from Superman: The Animated Series, but Neutron, a lesser known character from the comics, definitely counts. His role on the show was so minor, he doesn't even have a page on the wiki.
Some members of the Justice Society is slightly more well-known, but they are usually in an alternate dimension or something.
The friggin' Wonder Twins from Super Friends had their own episode.
Star Trek: Voyager, "Death Wish" When a being identifying himself as Q shows up wanting to die, we definitely expect John de Lancie to show up at some point. But who would have expected JDLQ to conjure up Will Riker to help him argue against Quinn's request to die?
The Strain (TV series) had an inversion. Joan Luss' children are saved from her by a group of Strigoi. Their leader, the only one who speaks, was assumed by many to be Quinlan from the novels, a Strigoi who was born as one instead of being an infected human. At the start of season two, it's revealed that the character is actually named Vaun. The character Quinlan does show up later in the season after Vaun is killed.
Even though he's a mainstay of the series today, Castiel's first appearance took everyone for a loop. In spite of all the mythical creatures and monsters Sam and Dean have run across, nobody ever imagined apocalyptic angels would be something they'd encounter.
Nobody expected that the brothers would ever team up with the Mystery Inc. gang of all characters, especially considering they're from an animated show targeted toward a completely different demographic.