MEDAKA BOX! The first thing I want to say is to just clarify things, before starting: Medaka Box is NOT a typical shonen, it is a parody-style shonen, which means it wants to parody shonen, through a shonen itself. And what do we get? Perfection! The perfect symbiosis between the two styles and the two targets, the one to tell a "normal" shonen story, and the one to mock it.
And how does Medaka Box do it? Through simple exaggeration and stereotypization.
First off we have Medaka, the typical shonen protagonist: already powerful, but with a lot to learn and a lot of things to expect him (her in this specific case). Aaand,well, she's like this in the first few chapters/arcs, before she becomes an unhuman monster, so powerful to seem not normal even for a manga (if we didn't know THIS exaggeration is absolutely part of the plan).
Then we have the story arcs: as usual, story arcs are structured following the "defeat an enemy>a more powerful one will approach" type of arcs, but it's not just like that; the grade of difficulty of Medaka and her group's adventures becomes more and more "abnormal" as the story goes, passing from challenges from normal people, to special, to abnormals and so on, and Medaka (and her group) receive sometimes a few powerup that seem maybe TOO random and unexplained *coffcoff shonen-stereotype coffcoff*
Talking about stereotypes specifically:
-Medaka Kurokami, the protagonist, a perfect girl capable of everything;
-Zenkichi Hitoyoshi, Medaka's normal childhood friend ("normal"..."""normal""", OK)
-Akune Kouki, the playboy of the situation. He was first a thug, then he met the goddess Medaka...
...and the ones i loved the most:
-Shiranui Hansode...there we have to stop for a moment. Well, other then being the typical cold tsundere loli with no feeling, no friend, that eats all the day and so on we have to appoint that her figure is a clear antithesys of that of Medaka;
-Kumagawa Misogi, the coolest character ever existed in the whole history of mangas! Ok, he's out of the stereotypes i guess, and he's more of an unconventional (but still parody-born) character. Being another antithesys of Medaka, he's born to lose, he's weak and human...and daaamn, he's perv!

Then we have exaggeration, that is a persistent way of parody in this work. The percentage of votes Medaka receives during the election, the number of abilities Ajimu Najimi possesses (10 billion) and so on, leading to an inevitable humor and often playing down during high tense moments.

I analyzed the parodian side, while I'm like disregarding the shonen side that is the one that permits Medaka Box not to be just a simple and repetitive parody. Infact, other then a funny parody side, the story told in this manga is well organized, original and fascinating, with nothing less than a Dragon Ball or a Naruto. Furthermore there's a gigantic number of different characters, every-one with its own personality, attitude and characterization.

PS:Sorry for talking too much and being not so well organized and polite...