flannel makes great batts---the loft of a batt is not a (right or wrong) some people like very flat thin quilts- some like them lofty---almost like comforters...it is a personal choice-
i've actually used a layer of muslin before for the center of my 'sandwich'= the project it was used for turned out great-
flannel is one of my favorites! adds good warmth without alot of bulk.
you can use anything you want- it's your project.