- Fanon Discontinuity: Similar to the later Jonny Quest vs. the Cyber Insects, this film is disliked by some fans. Common complaints include Zin's hideous and deformed appearance (due to his disease) and the claim that Rachel Quest's addition (to say nothing of Jessie) undermines the established relationship of Benton, Jonny, Race and Hadji.
- Although considering it's probable status at being an attempt of a reboot, it in a way already was a "What if" style origin.
- Hilarious in Hindsight: Despite the above complaints about Dr Zin's design, it still bears a close resemblance to The Venture Bros.' Dr. Z, who may or may not be him under a different name.
- Recycled Premise: Most of the story (dealing with Zin's clones and attempts at turning lead into gold) is original, however the Victor Devlon subplot is a new take from the "Deadly Junket" episode of The New Adventures of Jonny Quest, just with the twist that Jessie isn't actually the missing scientist's daughter this time.
YMMV / Jonny's Golden Quest