The #1 reason I don't use fast sinking lines in skinny water... I don't like snagging the bottom. I like to be able to fish the fly s-l-o-w-l-y when I need to and the intermediate provides that ability where the fast sink requires me to strip-strip-strip to keep it off the bottom.
The intermediate line fishes at an angle where the fly is the deepest object (except for the thickest belly portion if the fly has a lot of bouyancy). When fishing the deep eel on an intermediate, the fly could be the deepest object most of the time, and it can be on the sand where I like to fish flats stripers. I feel the take much better with an intermediate line, although most of the time it's the visual of the take that stands out.
I have also watched fish swim around a flourescent line on Monomoy, which wasn't soon forgotten. They don't make a fast sink clear line yet as far as I know.
Granted on the flats there are fewer snags to worry about than other places and a sinking line is critical when the flats are flooding and ebbing in the peak of a tide change.
My opinion, FWIW, is that you need both lines - and thus two spools: (a) hi-density line (b) intermediate line
A SW floater is a nice luxury for surface flies but most of the time I just tie it on intermediate and strip like hell.
Your results may vary,