Our school has 6th grade in Middle School with 7th and 8th. They are considering moving it to the elementary next year, and have sent home surveys about it. I'm not really sure what I think.
I went to 6th as part of elementary, and 7th and 8th were Junior High back then. I certainly think my life would have been worse in 6th grade if it had been in the Junior High -- 7th grade was bad enough! I went to a church school in 8th grade to escape from it, but then went to the regular High School.
My DS11 skipped 6th grade, although technically he was in mostly 6th grade classes during 5th last year. I don't know if it would have made any difference to him if it had been in the elementary.
The school is all on one campus -- elementary is in one building, MS/HS in another with some outbuildings as well, and after the construction they are starting in January, the elementary will be connected by hallway to the rest -- the cafeteria is for everyone, and the little kids have to go outside to get to it for lunch now.
Any thoughts on the subject? DD7 won't be worrying about it for several years.