Anti-Climax Boss: Bit's rematch against Leon in the Royal Cup Tournament was disappointingly brief, most likely due to the fact it took place towards the end of the episode. What could have been an epic confrontation between two evenly matched rivals turned out to be a quick and rather disappointing victory for Bit.
Jack Sisco is easily defeated by Bit in the Royal Cup Tournament in a fight that shamelessly recycles the same footage from their first battle. This was despite Bit failing to even touch him in their previous battle.
The Vega and the Berserk Fury were built up as all but unstoppable for most of their appearances, easily defeating the Blitz and Lightning Teams without any weapons or armor. In the Royal Cup, with the Berserk Fury's armor, Vega is defeated without much difficulty by the Liger Zero's basic unit in a fight where he struggles to land a single blow on Bit. This was despite the fact that in his debut, Vega had no difficulty hitting the much faster Lightning Saix and Liger Zero Jaeger.
Badass Decay: Jaime's Wild Eagle person is a One-Man Army in his debut that takes down dozens of Zabats on his own and nearly brought down a Whale King. In his later appearances, he's shot down in every single battle, and more often than not it's against ground targets.
Die for Our Ship: Two Words: Harry Champ. While not for Les Yay shippers (unless you count Leena/Naomi), he is often portrayed as an evil villain in Bit/Leena fanfiction, where he will resort to anything to get her, to the point of even becoming a rapist.
One of the most used Zoids fanfic plots involves a new character joining the Blitz team. It is not uncommon for this new character to be a Mary Sue of some sort; a gifted, multitalented pilot with a special, high-performance Zoid, which is frequently portrayed as an Ultimate X. Typically, the character will pilot a popular Zoid that never appeared in the New Century anime such as the König Wolf, Liger Zero X or Dark Spiner, or some kind of popular game variant Zoid like the Trinity Liger or Geno Hydra, though Custom Zoids are also commonly used. An Organoid partner is almost obligatory. Fanfics of this sort tend to exist simply for the author to showcase their badass fan character and/or custom Zoid; expect to see the canon characters reduced to background noise, jobbers, love interests or some combination of the former.
This type of Zoids fanfic plot involves taking the New Century characters and throwing them into a more "serious" plot reminiscent of Guardian Force, with the Blitz team getting drawn into some kind of epic, world-spanning conflict following the events of the Royal Cup, be it some asshole villain rampaging about in a powerful Zoid or a war between factions; a common trope is for the Blitz team to become "soldiers" and the Backdraft to become warmongers. Also expect to see plot devices from Chaotic Century suddenly crawling out of the woodwork, such as Organoids or the Death Saurer. Though Post-Royal Cup Doomfics were a dime a dozen back in the day, they aren't as ubiquitous as they used to be. However, they continue to litter the landscape of Zoids fanfic archives such as fanfiction.net and Anime Admirers.
Fanon: Quite popular, usually in the form of connections between New Century and Chaotic Century. For example, it's commonly accepted that Liger Zero is a further evolution of Van's Blade Liger and Zeke, and less commonly believed that the Berserk Fury is similarly Raven's Geno Breaker and Shadow, despite neither even being implied in the series (the former has more basis since Van's Liger does become the Liger Zero in the Chaotic Century manga but not the anime). The red Blade Liger is also believed by some to be Van's Liger and Zeke, if the Liger Zero isn't. The final battle in the series takes place near the wreck of a long-abandoned Ultrasaurus, which can easily be interpreted to be the one Moonbay used in the final battle of Chaotic Century.
Germans Love David Hasselhoff: New Century was a commercial flop in Japan, but when it was exported to the U.S. it was far more successful, doing even better in television ratings than Chaotic Century did.
Harry Champ. Often thought of as an expy for Thomas, he suffered a similar backlash. Though the character is a well-meaning albeit egotistical goofball in canon, many fans find him annoying, and he's often despised by Bit/Leena shippers, who tend to subject him to Ron the Death Eater status in fanfic (see above), taking him from "comically obsessed" to "evil stalker/rapist".
They Wasted a Perfectly Good Plot: There are actually a number of intriguing plot threads that go unresolved throughout the show's run. What happened to Leena and Leon's mother? How did the Backdraft Group come into immense power? Where the hell is the origins behind the Weapon X Zoids like the Liger Zero and Berserk Fury? These are introduced as major elements to the show's plot but are never expanded upon or even answered by the time everything wrapped up.