I prefer the nylon booties because the hole for the cleat is already there ... they just have the toe bit and that strap that goes under the shoe to hold the bootie in place.

The neoprene ones can be a pain because you've got to cut the hole out yourself (they provide a sort of template on the bottom of the bootie to help you), and then sometimes it doesn't line up properly which makes it harder to clip in and out. But they do protect the feet more.