Both positive and negative selection approaches have their advantages and disadvantages.
One of the main advantages of positive selection is that isolated cells are highly purified when compared to negative selection. This high purity is due to the specific antibodies used to target a particular cell type. Additionally, sequential isolations can be performed on positively selected cells. Many technologies, however, leave the positively selected cells bound to the antibodies or other labeling agents, which may affect some downstream assays.
On the other hand, negative selection produces targeted cells that are unbound by antibodies. Cell isolation protocols using negative selection are also quicker and easier than positive selection approaches. One disadvantage, though, is that negative selection methods are inherently less pure than positive selection methods, since it is more difficult to target all unwanted cells than one wanted cell population.