I prefer Totori myself, because I dislike (the character) Rorona in Meruru. They just butchered her. But I can fully accept that Meruru (the game) is an improvement in many ways.
Other things I prefer from Totori: The music, the atmosphere, the story, and the lead female.
On the other hand, Meruru has the infinitely superior cast all around, with most of the best characters from both games making an appearance and having a part to play. Save for Totori and Ceci, I found most of Totori's new cast to be rather dull; Meruru's new characters are almost universally better in that regard.