Let's talk fuel filtration, what systems are out there and does it make a large differance etc.. Here is one from Glacier Diesel Power: http://www.glacierdieselpower.com/product.asp?pf_id=MK20306-BLK
The Fass system has both types of filters on it. The stock filter system also has a fuel heater to help with filter waxing. If you bypass it, you would lose this advantage. GDP offers a filter/water separator system too. Multi-stage filtration is prefered. This is a good article on fuel filtration in diesel boats. boatdiesel.com/Articles/Articles.cfm?P=20060110_Introduction.cfm
The FASS units have provisions built in for a fuel heater. You can route coolant lines too and from the unit to heat the fuel. Personally, unless you are running Biodiesel, very few customers will need the fuel heater. Most customers that have been in cold climates for at least a winter use either winder blend diesel, fuel additives, or both. I do agree that you cannot over filter the fuel, especially on diesels. One of the big things I like about the FASS over the stock set up and some of the aftermarket set ups like GDP's set up, is you have larger filters on the FASS, easy filter changes, and you have both the water separator and fuel filter together, plus a pump. For the price, you really can't go wrong.