Anti-Climax Boss: Bit's rematch against Leon in the 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.
Die for Our Ship: Two Words: Harry Champ. While not for LesYay shippers, 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.
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.