Chaud is the biggest example. In the games, he's a Child Prodigy Official Net Battler who objects to Lan getting in his way; in the anime, he's got nothing to do with the Officials and instead is The Ace of competitive Net Battling. In the manga, he's a police agent, but, like in the anime, he plays the Always Someone Better card.
Bass is another good example. While his character ("become the strongest" + "destroy all humans") is roughly consistent between adaptations, NT Warrior comes at it from a radically different direction. In the anime, he's a reincarnation of PharaohMan.
Incidentally, PharaohMan, who in the games was largely just a high-level WWW guardian, has a massive God Complex in the anime that led him to try and conquer the world. When he breaks out of his can, he decides to take revenge on humanity.
Annetta was a completely different character in the anime; in the original games she was a brainwashed Well-Intentioned Extremist, while in the anime, she becomes a non-combatant ally of the Net Savers and a Love Interest of Chaud's (with a much darker back story to go along with Axess' Cerebus Syndrome).
Awesome Music: Shademan's theme from Axess. So much so that the Dub version used the same one as the Original version oddly enough.
Could be said of the series in general, once it hit its stride during Axess. The score during the original seasons were acceptable, with only a few notable themes. Sadly, more than likely because everyone had given up on it by then, the scores from Axess onward were never released - which is a shame, because that leaves fans attempting to sample songs for themselves.
As far as the dub goes, Dark Protoman's theme isn't bad at all.
Late in the second season of the anime, a "cat virus" escapes from a lab and proceeds to transform every Net Navi it encounters into cats. Simultaneously, Rush appears in the real world (which power he would go on to keep for the remainder of the show).
The entirety of the Mistman episode of Axess, which plays like the wierdest dream. Lan and Mayl (in clothing unique to the episode) go butterfly-hunting around the world (by running) only to find themselves in front of a massive pyramid, where Yuriko just so happens to be hunting for rare metal to make Dark Chips with. They all end up in a fight with MistMan, who ends up fighting for whichever side is holding his lamp. After the adventure ends, the entire pyramid disappears.
While the English Dub versus Sub wars of the show are currently minor, there are those who hates the Dub for its heavy editing and those who enjoys the Dub for fun.
Because of the divisive dub, fans are split on whether to refer the characters with their original Japanese names or their dub names. Those who watched the anime prefer the former while those who are more familiar with the games outside Japan usually prefer the latter, as long that the dub names are from the games themselves.
Among the two that focused on Cross Fusion (Axess and Stream), there's huge debate on which is better between them: those who hate Stream point to its pointless filler and overuse of cross fusion along with focusing a little too much on shipping while those who hate Axess point to it being gratuitously Darker and Edgier and its own filler. Hype Backlash didn't help.
There are some who don't like anything after the first two seasons, accusing it of having much darker tone and declaring that the new focus on Cross Fusion deviated too far from the original setting and plot of the games in favor of getting more humans involved.
Was the inclusion of the anime only character Tory/Tohru (Iceman's operator) pointless due to him having next to no major role after the first season or is he actually a good net battler and friend who is a victim of the writers writing him out. Ms. Yuri also counts: she was more re-characterized in the anime, but after Stream she and almost the whole Cross Fusion team were Demoted to Extra.
Complete Monster: Slur, The Dragon to Duo, is both a Knight Templarand a Complete Monster. Slur is fanatically devoted to exterminating all evil from the universe...where by "evil," she means everyone who doesn't agree with her master's extremely draconian concept of morality. In other words, Slur wants to kill all humans just because she doesn't like us. And unlike Duo, Slur has no sense of fair play - she deliberately "sabotages" the Humanity on Trial plot of Stream by giving Asteroid Navis to evil people, so that Duo will be convinced that Earth doesn't deserve to live. Vicious, sadistic, and with no redeeming qualities at all, Slur might very well be the vilest Battle Network villainess ever.
Princess Pride, in part for Adaptational Heroism and in part for adding some variety to Lan's love life.
Raika/Laika, who becomes a main character after Axess.
Fanon: Again, NT Warrior actually encompasses three different adaptations of the original Mega Man Battle Network. Fans like to mix-and-match details and canons. (Details on the YMMV page for Battle Network).
Fan-Preferred Couple: The anime (especially Stream) has a lot of closer-than-friends interactions between characters who don't even talk to each other in the games, resulting in a number of pairings below:
Lan/Mayl (along with Mega Man/Roll) * the only pairing that is carried over from the games, though Lan is clueless at first
Ms.Yuri/Dark Miyabi (Dusk)
Fanon: There is a debate about the Cross Fusion members being Net Savers. They are only referred to as "the cross fusion members" at the end of Beast where they are simply referred to as that and nowhere does it imply that they are Net Savers like Lan, Chaud, and Raika. In fact, it's implied that the Cross Fusion team don't even carry Synchro Chips with them normallynote In Beast, Zoan Gutsman attacks Dingo and Mayl and the two did nothing but dodge him while Lan, Chaud, and Laika fought. It is also popular to call them the Special Forces in some fan works even though they are never referred as that in the anime.
In Axess, Mayl dreams about Cross Fusing and attempts to do so, but fails. In Stream, she's able to Cross Fuse and helps Lan and Mega Man defeat Video Man and becomes a member of the Cross Fusion team with Roll.
In the dubbed version of the Axess finale, upon seeing Regal turning into Laser Man, Lan exclaims "Can everyone cross fuse?!". In Stream, several characters are given the ability to cross fuse.
In the manga, Dex is laughed at by the whole class when he brings up the civilization of Mu during a discussion on ancient civilizations. If only he knew.
Ho Yay: Netto and Enzan engage in quite a fair bit of this.
Jerkass Woobie: In Axess, Chaud himself suffered majorly when he was forced to use a Dark Chip on Protoman.EXE to save not only Lan and Anetta but Megaman as well. While Chaud was rather cold to Lan during their confrontation episodes later, you can't help but feel bad for the guy. Considering it Proto Soul Megaman that beat Shademan in the end, he likely feels using the dark chip only cost him his Net Navi.
Shade Man when the Darkloids ditch him in favor of Regal. When he returns to confront Regal, he actually fights partially in honor of the Darkloids.
Saiko when you consider what drove him to join Neo WWW. The company he worked for then participated in a navi car race and his boss put a lot of pressure on him not to lose (albeit without being a jerk) and when his original navi accidentally ruined the car, its clear he was under tremendous pressure.
Ivan Chillski only wanted to be a computer researcher and create a navi compression method until he was fired (albeit in a civilized manner) by his boss since the company was starting to run out of funds for his research and then Slur showed up with Asteroid Cold Man...
Misaimed Marketing: Even back then a lot of people thought that the show would have been a lot better off on Toonami than Kids' WB!, granted back then Kids WB was pretty much alive and well but still...
Mis-blamed: For some reason, people bash 4Kids Entertainment for the dub's quality. They had nothing to do with NT Warrior. All of the questionable aspects of the dub fall on either Viz Media or Kids WB.
Moral Event Horizon: While Duo judging planets on whether or not they should be destroyed already means he's likely crossed it well before the series began, It turns out that he crossed it when he destroyed his own planet, it wasn't for any good reason either, he just decided that he had the authority to judge whether entire species have the right to exist and felt that his creators didn't.
No Export for You: Battle Story never saw an English release aside from the original Japanese and translated to French. To make it more worse, it also got special chapters after the events of Battle Story which was never released outside Japan.
Only the Author Can Save Them Now: Stream. Duo, the ominous power hovering over the planet for most of the season, has the power to unmake and remake the entire planet and every human being on it. No way is any battle going to bridge that gap. So the writers reached out deep into left field.
Player Punch: PharaohMan's arrival at the end of the N1 Grand Prix. You can feel Lan's heartbreak watching him weep as MegaMan dies.
The Scrappy: Slur. Part of the hate for Stream is because of her invincibility, coupled with her prominence and how appallingly evil she is. Likely because of this the season ends with beingbrutally murdered by Bass.
Seasonal Rot: Every season can get accused of this. Axess gets accused of it for the shift in tone, Stream gets it for exaggerating it further, Beast Plus for basically becoming a stream of Filler. Every season has its fans, though.
Villain Decay: The WWW starts out as a fearsome organization bent on domination of both the real world and cyberspace. By the middle of the original show, they're running a curry shop together, where they have no qualms about cheerfully serving the heroes. They claim to be just as devoted to evil, though.
There's also Dr. Wily after the first season. He's absent in Axess, only getting mentioned a few times and comes back in Stream and appears to be homeless and has seemingly given up crime, however, unlike most villain decay examples, this does not overlap with badass decay as he's able to help out against Duo by deleting some of his life sized viruses with exploding cans, gives Ms. Yuri a regular Synchro Chip, gives Sci Lab blueprints for Dimensional Area converters.
In episodes 18-19, Maylu doesn't realize that O.O.C. Is Serious Business applies to Higsby, too, and so takes this vastly superior and vaguely described superchip he gives her and uses it on Roll (Roll also failed to suspect the chip at the time). She could get a pass on trusting a gift from Higsby, but she doesn't actually learn what the chip does, which means it's more of a liability to her battle strategy than an asset. Also, MegaMan being fooled into thinking that Roll is back to herself despite her form is not yet normal counts as this.
In Beast, Zoano NumberMan infiltrates Sci Lab, only for the real NumberMan to show up. No one can tell the difference between the real NumberMan and Zoano NumberMan until Iris mentions Zoanoroids being able to turn into beasts. Mayl and Roll devise a plan to attack both NumberMen and whoever turns into a beast is the Zoanoroid. It worked, but there were other ways to figure out the problem without exploiting NumberMan for a comedic moment, like asking questions only the regular NumberMan would know or examine their emblems since Zoanoroids have either Gregar or Falzar's symbol instead of a normal emblem. To add further into this, there was a Zoano Gutsman they were able to tell apart from the real one easily.
The Woobie: Poor Lan lost Megaman.EXE after he saved Protoman.exe from being deleted by Pharaohman.EXE. Thankfully Megaman was restored episodes later.