Mahoromatic feels so strange and bothers some people so much because it is a story that belongs in a Genre which is seldom seen in moderen lititure and not even listed for Anime, Tragedy.
The dictionary definition-
1 a : a medieval narrative poem or tale typically describing the downfall of a great man
b : a serious drama typically describing a conflict between the protagonist and a superior force (as destiny) and having a sorrowful or disastrous conclusion that elicits pity or terror
c : the literary genre of tragic dramas
What really lets it get to you as it starts out as comedy than transititions into a tragedy. I was always expecting something would happen to 'save' the situation 'cause no one wants a tragedy, especially in something that started out so fun. I was agonizing over it through the first nine episodes of season 2 (SMB) and distroyed when all the worst came. "How could they have done this?" was what filled my mind.