Zombie I know, but going back to the original question, Malory Towers is generally more popular because as a whole series and set if characters, it is more complete and satisfying than St Clare's.
So St Clare's devotes 3 books to the first year, then one to the 2nd, skips a year and then covers a year and has some more skips, whereas, Malory towers has a book per school year and goes right through to the end - it is a more complete and balanced coverage of a a school career.
Most people find Darryl a more convincing or stronger character to empathise with than the twins, who sometimes take more of a backseat within the stories and perhaps are less developed as characters.
There are lots of overlaps between the books, such as Americans, circus people, scholarship girls, French mistresses, scatty arty types, but Malory Towers by being written later just makes some of the characters stronger and run through the whole series more effectively. The addition of Darryls younger sister Felicity also allows more development of a younger year group alongside Darryls year in Malory Towers too, than is possible in St Clare's.
I think there are some fab sections to St Clare's and some great characters - Claudine and Antoinette Spring to mind, but Malory Towers has Gwendoline and there just isn't a nasty selfish character of her quality in St Clare's, nor an equivalent as good as Alicia and Darryl herself is never beaten.
Sorry if that's all rather detailed, but I saw this thread and just had to answer the original question - really enjoyed thinking about it.