Middle schools came about when researchers and psychologists discovered that middle schoolers may be better off with specialized, small learning communities, building relationships with a core of teachers and gradually building content and social knowledge while acknowledging the special emotional challenges of adolescence.
Turns out, some researchers disagree with this assessment.
The Brookings Institute in Washington, DC published a recent study recommending that schools "substantially improve" student achievement by moving to a K-8 model, and many schools are considering a move to either 6-12 or 7-12 model.
The report noted that in New York City and Florida, test scores of students entering a separate middle school declined markedly relative to the scores of students in K-8 schools.
Others argue that it is teaching methods that need to be adjusted, not which grades are housed together.
It is important to note that there are no major studies indicating what is best, one way or another. It is also important to note that "success" in these studies is measured solely by performance on standardized tests which have been proven to be substantially flawed measures of students' actual ability.
There is quite a bit of research indicating that the transition between 5th and 6th grade is very difficult and may be better handled if it is eliminated entirely or put off until 7th grade.
Personally, I feel that grade divisions are arbitrary and silly. I have known too many students who are years "ahead" in one subject or profoundly gifted in all and are held back because of their biological slot into a grade. I also taught in a school that refused to teach kids where they were; students who came in reading lower than their grade level were taught using on-grade materials and thus made no progress, were absent at much higher rates and transferred out of our school (perhaps that was the point). Students who were gifted got limited support in one subject area and were taught along with every other level in heterogeneous classrooms focused on making AYP.
Offer support - academic, emotional and social - along with high expectations (of parents and students) and it should not matter what grades are grouped in which configurations.