Bruce Wayne was originally depicted as merely Comfortably Well-Off. Now, he's one of the two richest men in The DCU. Batman himself has become increasingly ultra-competent and infallible in the past few decades. One could argue the flanderization of Batman was necessary to keep him interesting in the context of the Justice League. He's one of the few characters without a true super power, so the question of why they keep him around (aside from maybe his money) needs answering. Having him be the greatest strategist in existence gives him a purpose and even a reason for being one of the guys in charge.
Killer Croc was originally a somewhat intelligent gangster with a medical condition (a very severe medical condition), whose misanthropy was the result of being tormented by everyone (family included) for his freakish appearance. This was eventually downplayed, with Croc becoming more bestial and less intelligent as time went on (this was typically explained that his condition was worsening, further separating him from humanity). By the time of Hush, Croc could probably pass for a bulkier Alternate Company Equivalent of the Lizard (explained away by Hush infecting him with a virus that further increased his mutation).
He's also portrayed as the "brooding loner" of the Justice League. This is despite the fact that the "Bat-family" has more members than Superman's friends and allies, two of the five Robins have led the Teen Titans, one of those two also led Young Justice, the other is considered the most trustworthy man in the hero community, and Oracle acts as the Mission Control. He is a close friend of a lot of superheroes as well, and he managed to be something of a father to CassandraCain.
In 1983, Batman quit the Justice League and created a new team called the Outsiders after Superman saying he would not lead the League in saving Lucius Fox from being a hostage in a far away country for diplomatic reasons, and this lead to a dynamic within the DC Multiverse wherein Batman would be portrayed as a maverick and Superman a boy scout. While they patched things up later that year, 1986's The Dark Knight Returns (which took place in a possible future) made Batman the ultimate outlaw anti-hero, and Superman a tool for the Ronald Reagan of every political cartoon of the '80s. In the revised DC Universe, DC ran with this dynamic of Superman and Batman being at odds for about a decade before it just kind-of ran out of steam, though the recent Batman/Superman title and other New52 material revisited it.* The Dark Age of Comic Books is basically one huge flanderization of The Bronze Age of Comic Books, especially the "dark" contents.
When Superman was first introduced, he was a real scrapper and not afraid to get in the face of authority figures. That changed around World War II along with Batman, however by the end of the fifties, hew as flanderized into the ultimate boy scout and establishment figure. By the '80s, he'd become somewhat more morally ambiguous and a bit more cynical about people in power, especially after the Man of Steel reboot.
A notable aversion occurs with, of all people, Guy Gardner. Giffen and DeMatteis were concerned with how much Flanderization had already occurred with the character, who initially was more intelligent than Hal Jordan, but by the time of joining the JLI was mostly famous as a Jerk Ass with severe brain damage. A punch from Batman sends Guy into an alternate, hyper-sensitive persona, eventually revealed to be a total con, as Guy enjoyed screwing with his teammates. His girlfriend, Ice, sees through it.
The Justice League in general occasionally suffers this problem. The heroes in their own books have multi-faceted personalities, while Justice League in the hands of sloppy writers reduces them to their most stereotypical natures, such as Batman being completely unfeeling and methodical, or Superman's "boy scout" persona. This is in part because each character was originally The Hero in their own titles. They weren't developed with a group dynamic in mind so some of their key character development has also come from them playing off of each other in the team books.
The Ultimates are an interesting case of Flanderization. In their initial run, Mark Millar tended to take the most famous aspects of each Avenger (Cap being of the 40's, Tony's hedonism, Pym slapping Janet, Jan being slapped by Pym, Hulk's rage, etc) and amplified them all several times over (Cap was painfully old-fashioned in speech and social views, Tony was always drinking and/or flirting with some blonde, Pym was a textbook wife-beater, Jan was a textbook battered wife, and Hulk was a murdering cannibal). This went into overdrive when Jeph Loeb took over the third volume. Tony was always in a drunken stupor and Cap spontaneously picked fights over Wanda's choice of attire.
Johnny Storm started off as a somewhat-conceited daredevil hero of the team. Since the eighties, he's become increasingly more stupid and narcissistic, to the point where he now appears to be a ditzy, Ambiguously Gay metrosexual completely in love with himself.
Reed Richards was originally a tad eccentric and rather emotionally stunted, but was Flanderized in the late 1990s/2000s into a borderline savant who doesn't understand human social behavior. This pretty much is part and parcel of Reed's slow derailment from a many-layered, infamously trope-defying character into a generic scientific supergenius strawman. Perhaps most tellingly, Reed was originally written as a veteran of World War II before Comic Book Time forced the writers to cut that detail from his backstory. After 40 years of intense Flanderization, though, it's practically unthinkable that the current comics' pencil-necked nerd would have ever even considered serving in the Army, let alone that he would ever have fought in Nazi-occupied France in the Big One.
Inverted with the Thing: in his earliest appearances, he was a complete jerkass who was constantly picking fights with not only Johnny, but Reed, and had no use for people whom he felt were judging him. Later on, he was portrayed as more of a tough guy with a heart of gold.
Subverted with Invisible Woman who was originally called the Invisible Girl, and useless in a fight. She gained the ability to create force-fields, became a more competent fighter, took on the name Invisible Woman (after-all, Iceman and Spider-Man were supposed to be teenagers but never referred to as "boys") and has sometimes served as a more competent leader especially during such time as Reed was away.
Northstar of Marvel's Alpha Flight (later the X-Men) started off as an arrogant former athlete with an interest in politics and a devotion to his mentally ill sister. While John Byrne wasn't allowed to write Northstar as explicitly gay, he managed to work in a few hints. When Marvel finally got the bright idea to "out" Northstar... well, suddenly, it seemed like all that mature characterization vanished, and suddenly he was gay. Gay, gay, gay. So gay. Did he tell you how gay he is? Even worse, he went back to being a self-absorbed douche despite maturing over the course of Alpha Flight.
Even his powers became flanderized. At first, the idea behind his "quick healing factor" (note the word "quick") seemed to be that he simply healed faster than normal people. By some point, it was decreed that he could regenerate from a single-celled organism and was basically unkillable and therefore immortal.
Some readers complain about Surge. While she is initially depicted as being kind-of a Jerk Ass, it's understandable. While she was always an outspoken, rebellious smart ass, her later depictions make her much harder to sympathise with as she has been portrayed as an unrelenting bitch and it is becoming her most dominant characteristic.
Mojo was introduced in a miniseries as a psychotic Eldritch Abomination obsessed whose very presence actually caused living things to wither and die and who casually committed Mind Rape. He also commissioned genetically-engineered slaves to act in movies to entertain him. Even Doctor Strange feared what would happen if he stayed on Earth for long. As soon as he was brought into the main X-Men comics, the mystical powers and murderous demeanor were downplayed and the media obsession was turned Up to Eleven, so Mojo immediately became a comedic villain used to spoof the entertainment industry. He's still pretty damn horrible, though, and his comedic personality makes it worse when he does something like torturing Nocturne For the Evulz, or cheerfully sending someone to have their spine freaking removed.
The Hulk's raw power has been exaggerated to the point that he might as well just be a Super Saiyan. In his first appearance Hulk was perfectly capable of fluent speech and clear-minded reasoning. Over the years the "dumb" part of Dumb Muscle got amplified along with the "muscle", until we reach the iconic "HULK SMASH!" levels. Then, Peter David got the idea of explaining this as two different facets of Bruce Banner's fractured mind manifesting in different types of Hulk. How his level of strength tends to be inversely proportional to his intelligence has been explained by that his ability to reason tends to put limits to how much pure rage he can build up.
Iron Man used to be a fairly well-rounded character, being not only a super hero, but also a captain of industry, a millionaire playboy, a bit of a womanizer, a technological genius and - rather uniquely - physically crippled from his inception. He also had a bout with alcoholism. During Civil War, he got flanderized into a stubborn pseudo-fascist who'd just as soon throw his best friends in jail if they did not fall in line with the Super Human Registration Act. He had not nearly recovered from the fan-impact of that when Matt Fraction took him on an entirely different flanderization trip by reducing all his issues to side effects of alcoholism. Now, it seems Tony Stark spends approximately half the time agonizing about how badly he sucks.
Magica DeSpell's obsession with Scrooge McDuck's Number One Dime. Though her introduction does have her focused on attempting to steal it, other Carl Barks stories usually had Magica simply wanting to become rich, and would often have her working on schemes completely unrelated to the dime. Nowadays, she's completely psychotic about that coin, and you rarely, if ever, see a Magica story without it as her prime goal anymore. The dime itself also went through a sort of Flanderization. In the original story with Magica the dime had no initial magic powers. Magica just needed it as a spell component. Later writers seem to have missed this point and decided that the dime was somehow the source of Scrooge's wealth. In some stories, Scrooge can lose the dime over simple theft and suddenly his entire empire is crumbling. Don Rosamocks this in the Grand Finale of The Life and Times of Scrooge McDuck, where the Flanderization extends to rumors in-universe. Scrooge finds the idea that he owes his entire fortune to a lucky charm (which he had for twenty years before he even started to make his fortune!) incredibly insulting. That said, Rosa's take on the characters has also that Magica's spell would indeed work should she get her hands on the coin, and that losing the dime would indeed cause Scrooge to lose such spirit that he'd be no match for his enemies.
Booster Gold started as a well-meaning hero whose love of money often got him in over his head. Over the course of the '80s and '90s, writers forgot about the "well-meaning" part and turned him into a money-grubbing jerk. Thankfully, over the course of Infinite Crisis and 52 in the mid-'00s, DC built Booster back up, and now he's a genuine hero again—though the lure of fame and fortune still occasionally tempt him. Even better, he now intentionally acts like that, so no-one except Batman and Superman realises that he's grown into a competent hero in his own right, whilst he roams the timestream protecting history from enemies who — if they ever saw past his foolish reputation and realized he was the one foiling their schemes — would not only kill him but do it in such a way that Booster Gold never existed. So now instead of promoting himself, Booster must do everything in his power to make people think he's an inept idiot, in order to carry out his mission to defend time itself. Even before 52, some writers had started pointing out that there was more to Booster Gold than met the eye. At one point one of the other heroes muses that, being from the future, Booster must have been aware that Doomsday was a monster that was fully capable of killing Superman. And he still stepped up and took the first actual punch Doomsday aimed at a hero on his personal forcefield, to protect another member of the League. Both this acknowledgment and the moment itself hint that some people never completely forgot that Booster was kind of badass.
Archie Comics' Sonic the Hedgehog: Sonic's attitude has been cranked Up to Eleven, to the point where he's making wisecracks during a battle with Enerjak, a being with seemingly limitless energy (though this may have been more for comic relief than anything, it was a tad excessive). To be fair, though, it seems to have slightly boosted his Badass-ness—at the cost of emotion (again, though, to be fair, he never really showed much emotion anyway). The part about emotion is slowly being subverted as of #200; ever since Sonic's apparently driven Robotnik totally, droolingly insane, he seems to actually regret having broken down the guy so completely. An aversion may come from the early comics, which had a much zanier and cartoony format thus exaggerated a lot of the characters' traits compared to their SatAm counterparts, e.g. Sonic existed as a Karmic Trickster with a Totally Radical mannerisms akin to his AoStH counterpart, Sally's somewhat neurotic and no-nonsense attitude was exaggerated into a spoiled, mean-tempered prude and Robotnik was converted into even bigger a bumbling Card-Carrying Villain than his 'Eggman' incarnations. This was reversed as the comic's writing tone became more serious and akin to the show, though some genuine cases of flanderization do pop up on occasion.
Considering how often Cyclops and Havok end up fighting one another, they sometimes get Flanderized into being locked in an eternal Cain and Abel, being unable to abide one another at the best of times and one of them being a super-villain (usually Havok) at worst. This portrayal appears in the Ultimate, Legends, and Misfits universes, where (unlike their 616 counterparts) they don't need the influence of any psychic brainwashing to bait them into fighting.
Hank Pym (aka Ant-Man) has suffered from this perhaps more than any other Marvel character. During a single incident in which he was suffering a nervous breakdown, Hank struck his wife, Janet Van Dyne (The Wasp). Dozens of writers over the years have gone back to this time and again, with at least three different stories having been told about the two of them coming to terms with what happened. Hank's remorse is so Flanderized and extreme that he called himself the Wasp when she was thought to be dead. It's worth noting that both Spider-Man and Mr. Fantastic have hit their significant others in moments of extreme stress. While fans didn't much like either incident, neither character is regarded primarily as a "wife-beater" the way Pym is. And of course almost every female romantically tied to a superhero — whether she herself is super-powered or not — has struck her significant other, and none of those incidents have ever been exaggerated as a trait of the character. But that's a different problem entirely.
Cat Grant in Superman was introduced as sort of a Good Bad GirlBroken Bird. Someone who had a bit of an immoral past that she was trying to move beyond, and was looking for a good man like Clark Kent to be her anchor. Nowadays she's portrayed as a Lovable Sex Maniac at best and just Really Gets Around at worst. It's been mentioned that this is a facade Cat is using because of the pain of losing her son so many years ago.
When the Little Lulu comics first introduced Wilbur Van Snobbe, he was accurately depicted as a JerkassSpoiled Brat who would go out of his way to try to best either Lulu or Tubby, with no success. However, when the anime version was created, the creators took away his snobbish characteristics and turned him into a well-mannered rich boy who served as The Smart Guy to Lulu and the others. Then, when The Little Lulu Show was created, his snobbish personality was fortunately returned intact, just like in the original comics.
The Guardians Of The Universe in Green Lantern have always been distant and aloof, but were once wise and respected, having created an organization of star-patrolling peacekeepers that has survived for eons. With each passing year though, they become more incompetent, single-minded, and corrupt, lying to their members, holding their own mysterious agendas, and constantly having their mistakes blow up in the faces and inevitably needing to be saved by the Earth Lanterns (and then clearly resenting the aid). One comic even had a Guardian admit he didn't remember why they started the Corp in the first place. By this point, it's a genuine curiosity how they got an organization as advanced and well-functioning as the Green Lanterns working outside of dumb luck.
Dreadful Musician Cacofonix starts out as at least an average bard - Asterix blows off listening to his music once due to being busy (which annoyed him) and the people sitting near to his performance at the final banquet are cringing with their hands over their ears, but the villagers also perform a plot-important traditional dance to his music with every indication that they are enjoying it. As the comic progresses other characters (especially Fulliautomatix the blacksmith) start beating him up to prevent him from singing, which develops into a running gag, and he's shown to live in a hut at the top of a tree, where no-one can hear him. By the time Uderzo took over writing, he was so bad that he causes rain whenever he plays, which develops to the point where he ends up being so bad that merely playing a few notes creates an apocalyptic rainstorm that lasts for days.