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.
YMMV: The Wild Thornberrys
Broken Base: Not among Nickleodeon fans, but among professional zoologists. Some believe it is overly anthropomorphic and encourages dangerous attitudes towards animals, whilst others think that the anthropomorphism and breaks from reality are justified in order to get children interested about zoology.
Hollywood Homely: Eliza is actually really cute for a pig tailed, glasses wearing nerd. Especially in the later seasons where she lets her hair down and starts wearing more feminine clothing.
Granted, according to the book Not Just Cartoons: Nicktoons, this was more a case of Executive Meddling.
Lost in Medias Res: Because there was no "origin" episode, viewers were expected to simply assume that, for some reason, Eliza can talk to animals because of a Shaman and that they had a feral child named Donnie for no apparent reason. While the shaman was at least shown in the introduction, how they found Donnie wasn't explained until a Made-for-TV Movie.
And a more recent one, also concerning a Nigel Thornberry: combining his unintelligible gibberish from a random episode with a well-known song and then photoshopping his face onto the single/album cover. Blaaaaaarghghghgh.
This tendency has now extended to photoshopping his face onto gifs of scenes from Disney movies; later, this extended to any cartoon character and then even further, to anything that can be readily photoshopped (especially gifs where characters appear normally at first, turn away or hide their face temporarily, and return with Nigel's face). Example.SMASHING!◊
Seasonal Rot: From season 3 onward. The show starts focusing less on the animals and locales, and more about high jinks that just happen to involve talking to animals and may or may not feature Idiot Ball play. For comparison, season 2's "Chimp Off the Old Block" centres on the social structure of chimpanzees, and the show's finale "Eliza Unplugged" in season 5 centres on Eliza struggling to confess her love to a pop star.
The Scrappy: Tyler, Eliza's annoying and haughty cousin, who becomes a main character for part of season 3.
Shane also counts. Not only is he a completely unnecessary Satellite Love Interest for Eliza, but the audience is also supposed to like and agree with him despite the fact that he endangered not only himself, but Donnie and Eliza as well, a toddler and a preteen, respectively, and see him as being in the right when his only concern afterward was insulting Eliza, who was understandably furious at his incredibly reckless actions. And that's just his first episode.
Wheelchair Woobie: A character of the week was one. The conflict came from Eliza trying very hard not to seem like she's pitying her just because she's in a wheelchair, eventually annoying her.
The Woobie: Quite a few one-shot animals characters actually. Like the hyena from "No Laughing Matter", Emily the wombat from "Chew if By Sea", the rabbit from "Show Me The Bunny" or Tano the cheetah cub from "Cheetahs Never Prosper".