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.
Dexter/Buttercup, which carries on from the old intro tutorial from hints made in older Cartoon Network site games (like Cartoon Cartoon Summer Resort 4 and Toon Hoops) and announcer spiels during late 90s show credits (apparently Dexter likes Buttercup because she's sassy.)
Hilarious in Hindsight: Some time before Fusionfall came out, a fan called Bleedman started a doujinshi featuring an Anime-Styled version of the Powerpuff Girls and other Cartoon Network heroes fighting an Alien Invasion. Then Cartoon Network starts up a game featuring a bunch of Anime-Styled Cartoon Network heroes fighting an Alien Invasion... To be fair, Cartoon Network hasn't sued him or anything, and both are good in their own right.
That's putting it lightly; members of the dev team have flat out said that, early in the game's development, they wanted to hire Bleedman to help do the artwork. Didn't happen, but there's clear similarities in inspiration.
Attempts to promote live action shows like Unnatural History and Tower Prep through clothing for player characters weren't received well either. The backdraft was way less than for Johnny Test due to the items being temporary (for both getting and wearing). That and no elements from either series showed up besides the clothes.
Some of the Fusion spawn designs are pretty unnerving for an E+ game, for example the bear with a jackhammer for an arm. The concept art on the website is even worse. It's basically a PG version of the Zombie Apocalypse with Evil Twins running around.
There's also the disturbing implications of the fact that he's the only Ed Eddn Eddy character you see in the future.
The Scrappy: Johnny Test's presence in the game has not been well received. In addition to being from a fairly unpopular show in general, many people feel his presence is simply out of place because: A) He's not a Cartoon Network original creation like every other character/show presented, and B) He has no right to be around childhood characters like Samurai Jack or the Powerpuff Girls.