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.
The worst offender is Johnny Applesauce, with its "petitioning is better than violence" Ass Pull'd aesop despite the show itself being action-packed.
Lampshaded, averted and subverted in later seasonsnote (with the exception of X-Ray Johnny, where the "Books is knowledge, and knowledge is power" message is hammered in once a minute with no irony in sight; Johnny Applesauce pales in comparison.).
Broken Base: The show does have its fans considering it's been going for six seasons due to having some actually good dialogue, parental bonuses, and admittedly some clever plot lines; but, due to overexposure from its respective networks, stagnant character development, and way too much focus on Johnny, many have likewise taken a hating for it.
Cliché Storm: This show is criticized for rehashing a lot of stock cartoon plots, including its own.
Foe Yay: Bumper does this with Johnny a lot, whether Johnny is crossdressing or not; another example was in an episode where Johnny tries to change his personality in one of his sister's machines and, when he's stuck a smooth-talking British personality, Bumper implies to like this version of him a lot.
Fridge Horror: Altering DNA that often is likely to make most people wonder if it can have side effects in the long run.
Fridge Logic: In "Johnny and Dark Vegan's Battle Brawl Mania" Johnny and Dukey's game controllers somehow take control of Dark Vegan's suit even though they're not even wireless and are actually plugged into the game console.
Gil is noticeably always excited to see Johnny; yet when he sees Johnny's sisters, he can't even remember their names.
Mr. Black and Mr. White, whose Ho Yay is kind of blatant.
In the episode "Johnny McCool", at the end of the episode the twins are seen sighing at Gil eating a sandwich, then pans out to Gil sighing at Steve McCool, and it turns out it is a picnic. However the McCool presented is Dark Vegan in disguise.
Idiot Plot: There are a few episodes subjected to it here and there.
Iron Woobie: Dukey is pretty much this, still having his cheerful, lovable sense of humor despite being a Butt Monkey.
Johnny and Sissy look like siblings. Aside from that most likely unintentional instance, there's the writers' apparent fondness for Screw Yourself and everything related to it.
The scene towards the beginning of "Johnnyitis" in which Johnny, desperate to become sick in order to have an excuse to miss a big history test, eats a sick woman's used tissue. Said woman also had snot draining from her nose.
As of Season Five, Dukey now has the same voice actor as Johnny's Dad, which proved an unpopular decision at best; the same goes for the change of Mary's voice actress.
Season Two is this but that's mostly due to some fans being put off by the shift in animation after Season One; compared to Cyberchase and Caillou which had did similar but only after four seasons, JT at least had the common sense to switch early.
Though sadly by Season Five, the animation got even worse than before.
Susan and Mary Test are obviously the Dexters of the show, being redheaded genius children with a laboratory in their house.
Johnny is like Dee Dee, since both of them are Dumb Blonde annoyances who constantly cause trouble for their genius siblings.
Their parents are kind of like if you took Dexter's mom and dad and swapped their personalities, and then flanderized them. Johnny's Dad is a major neat-freak, while Dexter's Mom had her moments of this as well. Johnny's Mom is the head of the house and always working, while Dexter's Dad was just the head of the household.
Also, a female in the main cast is bothered by an Abhorrent Admirer, who is another nerdy genius child with their own laboratory. Bling-Bling Boy is the Mandark of the show.
Dukey can also be compared to Monkey, both being animals who have gained unusual ablities because of the genius children, Dukey's being talking, while Monkey becomes a superhero.
Uncanny Valley: Speed McCool and Monkey; although that's probably intentional.
The Deranged Animation (starting in season two and getting worse from there) and bizarre, strangely exaggerated facial expressions (along with most characters' lack of pupils) are surprisingly unsettling; none of this is helped by the unappealing (or just plain ugly in some cases) character designs.
Dukey, who always seems to get frozen in a block of ice or turned to stone. Also, the episode "Bathtime for Johnny" where Johnny "forgot" his birthday and he sobbed his heart out for nearly the whole episode (see Tear Jerker above). Last but not least, most people go out of their way in the show to point out how ugly he is.