Not having enough space to do it in. My sewing space is limited to the space between my bed and my closet, which is about 2 ft. x 8 ft. I don't even sew on an actual table...I sew on a TV tray. I lack the space for a decent sized table.
Other than that, sandwiching the layers is my least favorite. If its a huge project it takes me a few tries just to get it on straight and to get all the layers to lie flat. For my denim quilt just to accomplish sandwiching the layers I had to baste the batting to the back (after pinning both together), pin the top to that and quilt that, and then take all the basting stitches out (I'll never forget the thread color...hot pink).