I use both a 2.5 and a 3.0, just depends on the project. A true stitch in the ditch is exactly on the seam , so it "disappears " in the loft of the quilt. I usually use invisable thread either the clear or the smoke ( for darker fabrics) color depending on the project. If you are getting a bit of gathering loosen the top tension, especially if you are using the invisable thread. Also you should be using a top stitch needle. I have done a few projects that i did stich in the ditch with a metallic thread to highlight each 1 inch square. Still not sure if that was really worth the effort.
Some have the opinion that if you stitch exactly on the seam it could damage the threads in the seam. I have been Stiching in the ditch for 15 years and have never had any issue with seam damage.