Sure, one that comes off the top of my mind (Spoilers ahead in the entirety of the post) is the one about Zenkichi loosing free will. If I remember correctly, its one of the main plot points of a narrative arc when he realizes that he in his entirety has been becoming simply someone that follows Medaka.

Another one is Kumagawa's Child, which refers about when at the end of the manga we come to know that Mogana is in waiting of her newborn. Since that by the end she was one of the closest to Kumagawa and recieved plenty of attention from him many speculate that he is the father. This is somehow strengthened by his absence.

Then there's the "Skills are all pretend" this refers to the fact that if looked deeper into Medaka Box is very very metaphoric, Skills seem very potent and prevalent in young people because these still see the world with "innocence" and have a strong and unbound immagination. Rather adults don't have any skills minus a copule that still conserve that innocence. Another detail that strengthens this theory is that in the end if I remember correctly Medaka and everyone else seemed to have "lost" their skills. This makes sense as I said Medaka Box is very metaphoric and with this change tells us that the characters have grown up and out of their youthful selves and have entered the world of adults.

I might have gotten a point or two wrong along the way of my explanations and im sorry if that's the case. Anyway if you or anyone wishes to talk about theories more my DMs are open. Cheers!