One of the key differences between the Fernandes unit and the Sustainiac is the size of the pre-amp.
Sustainiac have been continually refining their product over the years to the point where the circuit board is very, very small compared to the Fernandes unit, which means you can get away with no routing on many guitars. Also, Alan Hoover at Sustainiac will work with you to determine exactly what switching scheme you want and the control setup you prefer, so you can get it more custom tailored to your needs.
For example, i ordered a Sustainiac Stealth Plus that i'm planning on putting in a project guitar i've been working on, and instead of mini-switches, i'm wiring it up with push-pull pots to turn the sustainer on/off and to activate the funamental/harmonic modes (i decided to forego the harmonic mix mode). Alan also provided me with all the wiring diagrams for my specific pickup setup and gave me lots of good advice before settling on my final order.
With Fernandes, you get what you get. Making changes or alterations to the way it comes out of the box is more difficult, and you probably won't get the kind of support Sustainiac gives.