Mamoru-kun ni Megami no Shukufuku wo!

Take a magically imbued school girl and mix in a short guy she can take advantage of. 

Honestly I cannot believe no one made this recommendation sooner. 1st thing I told all my buddies after seeing episode one was if claymore and mamoru had a kid it would be freezing. All three have rediculously powerful female characters that transcend the normal limits of their world's understanding. Likewise all three main heroines have a significant relationship with a male character that becomes significant to the heroines fate in the story. Freezing is kind of balence for the other two. Where Claymore has the intense combat scenes, Mamoru focuses on the heroines inexperience with men and trying to overcome that with her first love. Mamoru is mainly a school setting slice-of-life comedy with a touch of softcore ecchi. read more 

They are both romance stories in school, and both have some sort of a "magic" related theme to it. Plus the boy is much smaller than the girl. 

Similar magic and school setting. In Gakuen Alice it's called Alice and in Mamoru-kun it's Beatrice, both being abilities though Alices are much more specific. 

Without spoiling anything, let's just say these two anime are almost identical in how they play out. Very different male leads obviously, but everything else is bizarrely similar.  

Both have someone everyone respects who is perfect but has a kind heart 

Both series takes place at a school setting with students with special gifts and super powers. Of course, there's also the school idol that is literally almost perfect in everyone's eyes in both anime(s). Both of these anime series contain a lot of comedy and drama. Although Medaka Box lacks romance as of now, there are hints of flirtation from the cast.  

Despite the lack of superficial similarities in the plot or setting, these two shows are both light hearted and enjoyable romantic comedies. For people who enjoyed Mamoru-kun and are looking for another slightly overlooked, fun romantic comedy, I think Kamisama Kazoku fits the bill perfectly. 

Not really similiar in a sense, but there are a few things that are the same. In Gokujou Seitokai there is an essence of magic, also the presence of an almighty student council is in both of them. Not sure what it was that made me feel like they were the same, think its basicaly just the student council bit. 

Both have short male lead that is liked by a taller female lead character. The only difference is one deals with magic. 

-High school student council -Scary/easily angered girl in student council/main -Irresistible male main -love development between main -moe