15 years ago, I would use fread and "format" the data myself. I don't know how the technology evolved, but my guess is that fscanf, which is quite flexible and powerful, generates a significant overhead.
The list of functions dedicated to managing serial com. can be found here: http://www.mathworks.com/help/matlab/serial-port-devices.html
One additional point, do you really need to format the data "real time" as you receive it? Couldn't you just buffer it for a moment and then format the whole in one shot if really needed? On this matter, you could read the doc of fread, in particular the section about InputBufferSize.
EDIT after seeing your screenshot.
If you read directly 1501 floats with fscanf() or 1501*13 char or uint8 with fread(), you don't need the loop at all for reading the whole stream.
One thing that could happen in your profiling (but I am unsure now, because I've not been playing with serial coms for a long time) is that both fscanf() and fread() are blocking methods that won't return before they get the exact amount of data that you ask them to receive. So in all three cases, the 2.6x seconds that you are measuring are the time that it takes internally to receive 1501*13 bytes (for your bit-rate setting), plus a little overhead due to MATLAB processing. And the overhead is almost not visible because MALTAB format processing goes much faster than usual serial communications.
