The Filco is lighter, which is nice when I want to keep my keyboard in my lap (which is often). The LEDs in the Ducky's spacebar shine in my face when I lean back, which is really annoying, and leads me to keep them off 100% of the time. My USB-A to mini-B cable has some problems, but since the Filco has a non-detachable cable, these issues are not present. Filco does not twist as much as the Ducky in the "Twist test" but my black MJ2 makes some nasty creaking. Filco has more custom case options. Ducky's QC has been known to be lacking in some parts, mainly LED testing.
I could go on, but I just woke up and this post probably reads like crap.