Shikamaru in Naruto seems to suffer a little from this after becoming the leader for a short while. When in his function as squad leader he makes an effort not to appear his usual lazy self, his position as The Smart Guy is filled by Neji and he continued his streak of being the only member of the cast to not receive a major injury. After the timeskip he seems to have reverted back to his normal self but he still has a lot more boring outfit than anyone else in the Konoha 11, though he receives significant character development during his arc after the timeskip.
High School Of The Dead plays with this trope in regards to the main character Takashi. He worries that he’s got no real outstanding skills compared to the rest of the (useful) members of his team, yet given the flaky cohesion and variable sanity of the group, his ability to keep everyone on a leash is quite invaluable. The kicker is that while he may be the most centered of the group, he'’s not completely stable either and he knows it.
He's very worried about that last part. Takashi's aware of how much the others rely on him and knows that if he were to lose it, it would have a domino effect on the team and get everyone killed.
This is probably what crippled Seiya's popularity in Saint Seiya. Shiryu and Hyoga both get some focus at times and Ikki and Shun are practically Raoh and Toki as kids. Seiya gets the least amount of focus in terms of backgrounds, and even his quest to find his sister takes the back seat and is all but ignored for nearly fourteen manga volumesthe entire manga, being only solved at the end on a borderline Ass Pull.
The nominal leader (the one wearing the goggles) in any Digimon series, especially Tai. They're usually the most courageous and have the least issues, though the later ones verge more on Idiot Hero. Though this is notably averted with Takato who is the drastic opposite in that he lacks any confidence at the beginning of the story, and does get a good part of development. Then there's Taiki who is far by a super genius compared to the rest of the previous ones.
Voltron probably fills this trope most perfectly, as Keith is the standard reasonable and noble leader, while Lance was the hothead, Princess Allura was "the girl," Hunk was the "Gentle Giant," and Pidge was the "kid". He is the voice of reason amongst the varied personalities - he plays the role of the audience or writer that they can better empathize with.
Lampshaded in Sket Dance, where even though it's acknowledged that the Sket-dan wouldn't be able to exist without Bossun's leadership, he's considered really boring compared to the other-members in-universe as well as out. (For example, when an artist wants to created a manga based on the Sket-dan, he completely ignores Bossun, and later Bossun is the only one of the three who doesn't win an award in his class.)
Sasahara in Genshiken flirts with this trope during his tenure as club president. He's not as militant and flamboyant in his nerdiness as Madarame or as dedicated to his own special subgenre of nerdiness as Ohno or Tanaka, or as talented as Kosaka or Oguie, functioning instead as something of a peacemaker and diplomat among the group. Kugayama even lampshades this when he points out the irony that he attempts to spearhead the creation of a doujinshi (fan-comic) without even being able to draw. However, over the course of the series he discovers a bit of ambition and backbone and ultimately comes into his own as a character.
This is an explicit feature of Cyclops, leader of the X-Men. Joss Whedon described him as "the team washout in terms of popularity." The traits which make him, or anyone, a good leader are also the traits that make him the least fun at parties. To a certain extent, the two are mutually exclusive. Recent writers have given Cyclops a good deal of character development by embracing this trope.
Used to great effect at times, however, for comedy; being a standardized leader makes him adept at playing The Comically Serious role. It also helps that, depending on the writer, he has a very dry sense of humour.
Various events, especially the death of Jean and most recently Av X, have however lead to deconstructing this trope hard. As the only thing he had close to a personal life died, he basically through himself into work 24/7, and as mutants plummeted in numbers and things got Darker and Edgier, he pushed the team into darker territory to keep everyone safe, resulting in some morally ambiguous decisions. He's now frequently compared to Magneto (who he gave a spot on the team to when he came asking for a Heel-Face Turn), due to his willingness to use extreme measures others would find appalling or a last resort.
Nightwing/Dick Grayson, possibly the default guy for leadership in the DC universe, subverts this astoundingly by being one of the most popular characters. It probably helps that he has a very long, detailed, and sometimes painful history of growing up as a sidekick, and whenever he works with Batman he seems fine with letting Bats take the lead.
In any intelligently organized group he's a part of, Batman will be the leader (or, at worst, co-leader) either overtly or covertly, so it's more a matter of Dick being smart enough to know that.
For the DCU as a whole, Superman often takes this role, due to him essentially playing the role of role model to all other heroes. Over in the Marvel Universe, Captain America plays this role for mostly the same reasons; while Nick Fury often has more authority than him, Fury's also a world-class Jerk Ass that makes him slightly more distinctive.
Jake from Animorphs. While he seems like this to his teammates, his inner conflicts resulting from his position and Shoot the Dog tendencies make him a subversion of this trope. This is especially brought to light when he orders his (Yeerk-infested) brother killed and starts committing war crimes against the Yeerks.
Tom Corbett, Space Cadet. Despite being the title character, a clean-cut all-American boy and The Smart Guy, his negligible personality is overwhelmed by those of his much more colorful and assertive teammates.
Bridei of Juliet Marillier's Bridei Chronicles.
Rand, the hero of The Wheel of Time, is pretty bland. His two best friends have far more unique personalities.
Rand is arguably a deconstruction of both this and The Chosen One, since for much of the later part of the series, he was literally going insane as a result of all the pressure he was under. He did finally get better, though, and now acts more like a wise beyond his years holy warrior than anything.
Rhodan, the eponymous character of the long running Perry Rhodan pulp space opera. Much was made of his leadership and decisiveness in the early years, but that eventually got old and now he's basically the reader's projection screen.
Jason and the Argonauts: Apollonius of Rhodes' take was fresh-faced kid Jason with no exploits to his name, is put in charge of this all-star team of established Greek heroes. He can't help but come across as bland in comparison.
Kill time or die trying: Brad from Part I is a fairly generic student who cements himself as the moral compass of WARP and eventually becomes club president.
Firefly averts this trope by showing Captain Mal Reynolds as heavily conflicted with personal demons and prejudices. He is morally gray, (or at least adheres to his own code), has a hotter temper than both his lancer Zoe, and his Big Guy, Jayne (both of whom have fairly hot tempers themselves), and is arguably the most interesting of the main characters on the show.
Jack of LOST was never without his own issues, but because he had to fulfill the role of Wasteland Elder, he never seemed to face his problems head on and develop like his followers. Eventually, he does manage to subvert the trope, when after finally leaving the island, his personal demons follow him and escalate, and he slowly falls apart. The fandom seems to like him now.
Star Trek: The Original Series, especially in the early episodes, frequently played up the idea that Kirk (or any Starfleet captain) was obliged to make sure the crew perceived him this way—seeing him as always unflappable and dependable, to ensure order on board ship. According to the writer's bible, the reason Kirk plays so hard and gets into so many romantic entaglements when he's off the ship is to relieve the stress of maintaining this idealized image when on board.
Which is in direct contrast to Jayden's Samurai Sentai Shinkenger counterpart; Takeru Shiba, who is somewhat of a subversion by the fact that he appears to try and keep up the trappings of a Standardized Leader but eventually slips more and more as his backstory is revealed. It becomes one of the centerpoints for the latter parts of the show.
Despite not being a single main protagonist (for there isn't one), Mike can fit this in The Young Ones. He's not standard in any way, but compared to the craziness of Neil, Rick, and Vyvyan, Mike seems much calmer and notably less funny (and by extension, popular). However, he leads the housemates into many of the main events and rather than acting as an audience surrogate, he acts as a set up for some of the jokes, without causing as many laughs himself. He is also involved in barely any of the slapstick violence compared to the other three, but he is usually in charge of what happens in the "story". A lot of people don't think much of Mike, but he provides a contrast that make the other three so funny.
In most RPGs, the PC (player-created or otherwise) is this character. Such tropes as AFGNCAAP and Heroic Mime come under this trope, so examples include Link, most Final Fantasy or Fire Emblem player characters, and nearly all characters on those two pages.
In fact, the Bioware games go to almost the exact opposite of this trope, acknowledging that the player's character becomes an awe-inspiring demigod before the first story's even over, leaving plenty of room for the world to be even more impressed in the sequels. The player's uncanny and sometimes unlikely ability to lead (despite whatever other flaws they might have) is just as often called out.
Isaac, the (first) protagonist of Golden Sun, fits this trope to a T. In the first game, it's apparent from the way people talk about you and ask for your advice that you're the Only Sane Man of the group, and when he gets his own lines in The Lost Age he comes off as, more or less, Scott Summers of the X-Men.
Lars Halford of Brütal Legend is an intentional example. A charismatic leader who lacks any skill other than leadership, it's only Eddie Riggs' talents as a Roadie that actually kicks his revolution into high gear. Also, his flaunting of his Big Good status to Big Bad Doviculus gets him killed automatically.
While not an example of this in the main platformers since there's never any team to lead, Mario fulfills this role in the RPG spinoffs, which generally feature very quirky party members in contrast to his intentionally flat character seen across all media.
In Borderlands 2, Roland fulfills this role for the Crimson Raiders and the former Vault Hunters, as both the leader of the resistance and as the Straight Man to his companions.
Discussed in Joe Loves Crappy Movies, where they decide that the appropriate title for Leonardo and Cyclops is "Jacktard"
Mark, while far from leading the cast of weregeek, is The Hero and protagonist. His only real trait is his burgeoning geekiness, and his naivety. The other members of the cast get way more personality.
Matt O'Morph, while not particularly powerful, is the team leader in Everyday Heroes. This is mainly due to administrative competence, people skills, and seniority.
Mostly averted in Homestuck. The main protagonists, John, Karkat, and Jane are all leaders of their sessions, but have just as many quirks and foibles as anyone else, though they all are kind leaders. The Royalty of Derse and Prospit on the other hand are flat and have little personality aside from being leaders, but to be fair the Kings are only mentioned in passing a couple of times. The Queens are more interesting, but still fit the trope pretty well.
Leonardo is this in some incarnations of the Teenage Mutant Ninja Turtles, most notably in the 80 cartoon. His 2003 incarnation, on the other hand, subverts this trope. His 2012 incarnation actually seems to be inverting he trope.
The Toxic Avenger ("Toxie") in the short-lived cartoon Toxic Crusaders. He was big, strong, ugly, and had a sort of spider-sense. All the other Crusaders were also big, strong, and ugly, plus they had quirky, unique, useful powers. It didn't help that Toxie had almost no personality, and his action figure was incredibly boring compared to the lavish designs and arsenals of accessories that the other characters in the toyline got.
In Teen Titans Robin has a weird relationship with this trope. If he's not the focal character of an episode, he'll usually play this trope very straight, but when he does take the spotlight, we get a pretty good look at his imperfections. In fact, Robin's major flaw is that he takes his job as the team's leader too seriously; he'll become so obsessed with defeating a villain (usually his Arch-Enemy Slade) that he'll do anything, no matter how reckless, to bring them down, and will often become shockingly insensitive to his friends' feelings in the process.
He's also considered the "coolest" member his team by the alien princess, the cyborg, the shapeshifter, and the half-demon witch. The Aesop of the episode where we learned this was him learning that he doesn't have to be the best at everything, and he shouldn't take things personally.
Word of God is that he was visually designed to be appealing to teenagers. For example, the big, clumsy feet represent how teenagers may feel about their changing bodies. He's also somewhat vain about his hair.
"As much as I hate to admit it, he and I are kind of alike. But there's one big difference between me and Slade: he doesn't have any friends."
Averted in the successor series Teen Titans Go!, where Robin has the Idiot Ball superglued to his body and is mainly leader only because anyone else (except possibly Cyborg, who in this series functions as a mentor or co-leader) as leader would be worse (in one episode, Beast Boy becomes the "Alpha Male" ... somehow ... and he, Starfire, and Raven begin acting like gorillas).
Ken Washio from Gatchaman (named Mark in Battle of the Planets).
Some of the later shows and movies try to remedy this, to the point where the Fred in one incarnation can seem like a totally different character from the Fred in another.
Most notably averted in Scooby-Doo: Mystery Incorporated, which turns him into a world-class Cloudcuckoolander — with the same voice actor as in the original 1969 show, making it all the more jarring.
Captain Planet and the Planeteers showcased this immensely. Even though Cap himself took over when the powers combined, Kwame was technically the unofficial leader of the crew when the mullet wasn't around. And as mentioned before, he suffered from lack of personality and had no depth whatsoever, compared to Wheeler, who while impulsive and had a "never say die" attitude, was apparently a little too gung-ho and non-level headed enough to be leader of the Planeteers. Kwame was basically there to be superior to Wheeler and... that's about it. He was not helped by the fact that he had very few lines in many late episodes, apart from Stock Footage. Levar Burton got popular and expensive, and they used him less and less, but his character was still there, following the others around like a ghost until it was time to call Cap.
Hank the Ranger in Dungeons & Dragons fulfills the trope so well that when one episode tries to present him as a traitor to the group, it's entirely unconvincing and falls epically flat.
Leader-1 in Challenge of the GoBots was (obviously) the leader of the Guardian Gobots. He was also the most flat and uninteresting of the protagonists, to the point where one had to assume that he was only the leader because his name was Leader-1.
In Futurama Professor Farnsworth describes the leader of his first ever crew as a "dedicated young man with no characteristics".
It's deliberately invoked with Optimus in Transformers Prime. It's explicitly stated that Primes are expected to act like this.
To a certain degree, it's deconstructed. It mentioned several times that Optimus is a compassionate and noble leader but doesn't socialize much or have a sense of humor. Arcee and Bulkhead have said that the responsbility of being a leader weighs heavily upon an individual. Ratchet points out that Optimus was different before he became a Prime and was similar to Jack.
Optimus Prime in all his forms (possibly excepting the Transformers Animated version) cannot be tainted to The Dark Side. The fact that he's also one of the more imposing and martially skilled Autobots might make this something of a subversion; just putting Prime on the field will rout most Decepticon cannon fodder (unless they can occupy themselves by going after his subordinates, which might keep Megatron from killing them later). More modern incarnations outright specify that Prime being such a beacon of purity and hope is his greatest weakness, he is so adament about protecting innocents (such as humans) that he forgoes his own survival instincts.
Deliberately invoked with the Transformers Prime version. Ratchet described 'pre-Prime' Optimus as being more like Jack. Apparently becoming a Prime alters one's personality to fit this trope.
Recent works also seem to be moving Prime into being a deconstruction of this trope; the IDW comics in particular go out of their way to show how much stress, mental trauma, pain, and difficulty one would have to go through to be the Standardized Leader and take care of everyone.
Prime has, however, generally managed to dodge the "audiences don't latch onto him" that often goes with this.