Comparing this to SpongeBob is like comparing Titan Maximum to Megas XLR because they both involve robots. THEY ARE NOTHING ALIKE.
While I prefer Flapjack greatly, I'm not going to criticize SpongeBob. Instead, I'm going to state the actual reasons why I believe Flapjack is one of the greatest cartoons to come out since the days of Cartoon Cartoons.
Firstly, the art. The art style is simplistic, but works well. What really adds character to the show is the grotesque close-ups and surreal scenes which give the show a great amount of character and flavor. While attempting to avoid SpongeBob criticism, I may as well point out how SpongeBob completely lacks the former, and isn't heavy on the latter, opting instead for a more conventional type of animation.
Second, the humor could not be any more different from SpongeBob. The plotlines typically choose to mix sitcom ideas with an underwater setting and the humor mixes slapstick and child-aimed humor (and in the earlier episodes, a good deal of innuendo). This show is very, VERY dark for a kids show in a nautical setting, tackling drunkenness, drug (candy) addiction, death, disease, kidnapping, dismemberment, and child neglect (in an ironic fashion). The show also features innuendo and surreality.
The characters are also different, and the amount of personality. While some may compare Flapjack to Spongebob based upon the fact that they are both incredibly happy, Flapjack is more naive, childish, and shows many differences. Bubbie and K'nuckles are parental figures to the boy, unlike the, oddly enough, chosen comparisons. Most characters, including secondary ones, are quite fleshed out, with episodes dedicated to backstories and development of characters.
All in all, Flapjack was and still is a wonderfully unique show with a darker flair than most children's cartoons, a very well-done art style and deep characters. Regardless of one's opinion on it, it deserves to be judged on its own as it simply cannot be compared to any other show (the closest would be Regular Show, but that lacks the feeling of horror, replacing it with conversational dialogue)