Himawari!

Similarities: Both have the same male teacher to female student arc. Both male teachers found themselves teaching in some very wierd school and often found themselves getting into all kinds of trouble with the students. Disimilarites: The teacher in one anime has to be wary of one students whom he did something stupid to, while the other has to be wary of all students who were out to kill him except one who always saves his life.  

Two energetic girls are present as the main protagonist in these two series. On the other hand, there's the main male protagonist who has a strange relationship with her. Throughout each episode, they show a deeper care for one another that borders on romance. There are also other girls with different personalities as well but all have a passion for fighting and the ninja arts in both series. Although neither series are any special or great, they do pass the time with their comedy, drama, action, and amusing scenes. 

An all-girls class of ninjas are forbidden from coming in contact with boys. In Himawari, they are just banned from the neighboring boy's ninja school while in Kunoichi Tsubaki no Mune no Uchi they are banned from all men. Both shows feature supernatural-style ninjutsu. 

Both series are about ninjas. 

In this comedy a ninja protects a clumsy moron they are in love with. But this time the ninja is the female and the clumsy moron is the male. Think of this anime with a role reversal. Same very cute romantic comedy of ninjas and their accident prone love interest. Himawari protects her teacher whom she is CONVINCED is a skilled and wise master, in reality he is an incompetent boob but her love goggles won't let her see that.  

Himawari! is the more serious of the two, but it's still a comedy about a kunoichi in training. Watch Himawari! if you want more bite in the story. If you like ninja nonsense and shenanigans galore however, 2x2 Shinobuden is the one to watch.