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.
Arc Fatigue: It's already settling in by the time we get to the Velgmon and Cherubimon arcs, but by the time the Royal Knights arc comes around, some fans just put their foot down or skip to the ending.
However, other people see it as a good deviation, since it led to the digidestined strategizing more and actually fighting themselves instead of others doing for them. That's why the Take That lower on the page exists, the writers may have wanted to make the human children less passive.
Badass Decay: Seraphimon, when the cast rescues him, holds his own against Cherubimon's henchman at first, until Mercurymon beats him easily by making his attack rebound on himself, turning him into a Digiegg. Compare this with how his evolutionary line was portrayed in Adventure - even in Adventure 02, Angemon and Magnaangemon were extremely competent at their own level, with the former able to fight on par with an Ultimate and the latter being able to easily dominate over a Mega
Invincible Villain: Duskmon, having the Spirit of Darkness, blows every other Spirit Hybrid out of the water. Every single one. This, unfortunately, reduces his import as a character in his earlier appearances and instead makes him simply an obstacle. It gets better.
The Royal Knights spend the entire arc easily beating the crap out of the heroes each time they meet them and successfully reaching their goal in every episode until Lucemon finally arrives (which took nine episode), and when they finally bit the dust, it's only because they forgot to level grind. This quickly becomes so predictable it's painful to watch, and some fans just skip to Lucemon's arrival at this point.
Fan Preferred Pairing: Although Takuya and Izumi got the most Ship Tease, in the Japanese fandom, they're not often paired with each other. Izumi tends to be paired with Kouji or Kouichi. The Takuya / Zoe pairing is probably the most popular in America though
Hilarious in Hindsight: The Elemental Powers of the first five Chosen Children? Same as those of the Five-Man Band from Smile Pretty Cure!, only the elements of the leader and the lancer are swapped. As if that wasn't enough, one of Smile's villains is a Wolf Man with a color palette mostly in cool colors (just like Wolfmon/Lobomon and Beowulfmon) and often gets paired with the light-elemental heroine in fanart.
The initial digivolutions are done by the team running their digivices along their hand... which Power Rangers Operation Overdrive did in 2007 (OK, Overdrive ran it along their arm, but close enough).
Tai's Voice Actor, Joshua Seth, voiced a Wizardmon in one episode. When Seth retired from voice acting in 2005, some of his pursuits included being a comedian, hypnotist, and... magician. Really, he did.
So the whole story starts when a group of kids gets a bunch of weird messages on their phones that leads them to the Shibuya train station... heeeeey, wait a minute!
Moral Event Horizon: When Lucemon absorbs Koichi's data following Loweemon / Koichi's Heroic Sacrifice to save the others from his Ultimate Sacrifice attack, Takuya officially announces that Lucemon has gone too far beyond the line. Cue the first appearance of Susanoomon afterwards.
Really, almost anything Lucemon does is this. Prior to the series with his corruption of Cherubimon, driving him to gather all the data in the Digital World so he could absorb it and escape his prison, leading to all the destruction he caused during the series. And after he's freed, despite Dynasmon and Crusadermon's loyalty to him, he absorbs their data after their defeat to grow stronger, not content with power he already possessed.
They Changed It, Now It Sucks: Removing the Digimon partner's was the biggest issue for most people in the series. Instead the characters were more like Power Rangers then Digimon characters which combined with the whole Broken Base, really adds more fuel to the fire.
They Wasted a Perfectly Good Character: A Gallantmon appears as cameo in Autumn Leaf Fairs. That's right a cameo, without any lines, in a series which introduced the freaking Royal Knights! The American dub fix this a bit where the Gallantmon speaks in the same manner as in Tamers and even refers to itself in the plural as a definite Shout-Out to Tamers, but that's still not much.
Takuya and Kouji outshine everybody. Yes, other seasons usually have The Hero and The Lancer gain the highest evolutionary forms, but this series takes the cake. What makes it worse that the beast and human fusion hybrids for the other Chosen spirits DO exist for the others, and putting them in would be hardly unreasonable.
The four spirits used by the villains, later reclaimed by the heroes, are never used again. Epileptic Trees would have you believe that the four kids encountered later in the series; Chaiki, Katsuharu, Teppei and Teruo, were intended as candidates for them.
The Beast Spirits become Outof Focus for the second half of the series, and don't even appear in the final episodes.
The Royal Knights. The group is far larger than the two Lucemon sent out to claim data. Baromon hints that they were well known, but this is never brought up again.
The Digital World's relationship with the Human World, something that was a key point for every other season, is never elaborated on.
The conflict between the Human-type and Beast-type Digimon, according to the backstory for Cherubimon, is supposed to be an ongoing war by the time the series begins, yet it is never elaborated on aside from a single movie, and a non-serial one to boot.
The Untwist: Lucemon was behind Cherubimon's actions. Given how the series decides to get mentioning him when revealing some of the backstory, it's no surprise that he plays at least some role.
Values Dissonance: Japanese divorce laws are very different from those in other countries. As a result, Koji's father hiding Koichi's existence, pretending that the twins' biological mother is dead, and effectively cutting off that side of the family comes off as a lot more of a jerk move overseas. The American dub does try to lighten this up by softening some of his dialogue about Koji's birth mother and stepmother.
Sakkakumon, known as Sephirotmon in Japan, is shaped like the 10 aspects of God in Judaism, the Sephirot. Fittingly, that's the same number as legendary warrior spirits; and each orb contains one enemy corresponding with one of the ten elements. One of these orbs contains Mercuremon. Yes. Mercuremon exists inside himself.
Lucemon is full of symbolism. Not only is he clearly inspired by Lucifernote His name derives from the French word for "light", his attack is called "Paradise Lost Punch". Also, he has what looks like a Dharmachakra (Buddhist Wheel Symbol) on his chest in Chaos Mode.
Woolseyism: A name was needed for Tommy/Tomoki's brother, simply called "big brother" in the Japanese version. Instead of pulling a Keenan Crier and making one up out of whole cloth, they chose "Yutaka." Not only is this an actual Japanese name, it's an anagram of Takuya, alluding to the deep friendship between him and Tomoki — Tomoki even calls Takuya "big brother."
Some people actually like that LordKnightmon was renamed Crusadermon and made female.
WTH, Casting Agency?: Occasionally, the dub can get weird with this. Snimon sounds like Myotismon from Adventure, Cherubimon like Leomon from the same, and a Toucanmon and Mushroomon sound like they're channeling Kazu from Tamers and Davis from Adventure 02, respectively.