Honestly, this has been addressed to a great extent, but it still comes down to a matter of preference. Both systems work as well as the person operating each. For example one guy may make incompletely cracked or wet biodiesel (like me when I'm in a hurry), which can cause problems in the engine, same is true with WVO (waste) and SVO ((straight) veggie oil.) A crappy installation or improperly filtered WVO and ya got problems, right?
I'm a processor, in part because that is what I learned, and at considerable effort, I have my effort at stake. I have mastered many technical fields in my day, one such study was DOS
http://en.wikipedia.org/wiki/DOS, I can't afford to let any more efforts on my part go obsolete.
In summary, it isn't so much about which is better, more about with what the user is comfortable.
I ain't scared of potassium hydroxide, I am very careful with this extremely toxic substance though. I suggest building an outbuilding for the processor, to be safe and keep this stuff away from your family.
I've got some information on my site
http://outfitnm.com/alt-energy/biodiesel Well perhaps more than a little info
Those that know Brian know he hasn't a short story in him
My sig on biodiesel.infopop is: Home of the biodiesel eating bears