I use circularity quite a bit. The formula I use is the inverse of the one you use:
circularity = (Perimeter .^ 2) ./ (4 * pi * area);
so for me the circularity of a circle is 1 and the higher it goes, the less circular it it. For you the lower it goes (closer to zero) the less circular the blob is. You can do it either way.
I don't often use eccentricity because you can get the same eccentricity for a perfectly smooth ellipse as for some tortuous-shaped blob because it fits the perimeter shape to an ellipse. For example an asterisk and a disc might both have the same eccentricity but there is a dramatic difference in shape that is not picked up by eccentricity. Don't use eccentricity unless you know that your blobs are fairly close to ellipses.