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These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
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 lead 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 Intentiond 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).
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 raremetal 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.
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 Big Bad 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.
Crack Pairing/Les Yay: Serenade and Slur. Genderdebates aside, these two are often paired together despite never met at all (Serenade in the manga and BN3, Slur in the anime). Although this is probably because both of them are elite-tier and feminine looking Navis so they are often shipped together like rivals. Some fans even slipped Bass into the pairing and make those two fighting for his affection as well.
Crowning Moment of Funny: Possibly when Yai prevents Maddy from winning a net battle by reflecting the sun off of her large, waxed forehead, blinding her.
Crowning Music of Awesome: 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.
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 Discontinuity: Some fans pretend there is nothing after Axess (which may have something to do with the lack of localization). Others just refuse to acknowledge anything past the original series. Some fans did not take kindly to cross fusion at all.
Franchise Killer: Stream, likely for its massive deviations from the original plot and setting. Beast involved an obvious attempt to cull the wayward Sentai tropesnote Reducing the Henshin Hero cast to only Lan, Chaud, and Laika; involving more of the Cyberworld; integrating more elements from the video games, like widespread use of Copyroids and even allowing other Navis to Beast Out; etc., but the series was obviously on the way out by that point: Beast had about half as many episodes as Stream. Beast+ had a similar number of episodes, but only about ten minutes each.
Ho Yay: Netto and Enzan engage in quite a fair bit of this.
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...
Misblamed: People bash 4Kids for the dub's quality even though they had nothing to do with the anime's dub other than airing it.
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.
Clarification: 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.
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 it's 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 season 1, 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.
What an Idiot: In episodes 18-19, Maylu putting on the chip without knowing of the effects on Roll. Additionally, Roll herself didn't try to get suspicious on the chip she has at the time.
Also, MegaMan being fooled into thinking that Roll is back to herself despite her form is not yet normal counts as 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 to feel bad for the guy.