Much of the similarity between these two are reflected through the titles themselves! Both are set in a realm of magic, within a (very Hogwarts-y) magical institute, and the young female leads are incredibly similar 'happy witches'. The central trio of best friends in both series are also alike.
Little Witch is the lighter of the two with some great and endearing comedic moments. And, due to its short length, it does not get as much exploration of the characters or the world (both of which are utterly fascinating) as Mahou Shoujo-tai, or Tweeny Witches. At 20 episode, the latter does very well in that regard and also delves into some unexpected yet interesting themes.
Both are wonderfully creative and a very enjoyable watch.