I am not a fan of invisible thread. I've used several different brands and I just don't like the way it looks. But, like you, I hate to change the thread for each fabric color. So, the last time I did applique, I used black thread around all the applique and I really liked the look. My project was a appliqued baby quilt. I am getting ready to do another baby quilt with applique butterflies and I plan on stitching around the appliques with the same color of thread that is in the border fabric.
I use regular thread in the bobbin in the same color that I use in the needle.