I guess each has its partisans.
When I started out with the E3D, it seemed to be harder to use than my (old ceramic) Ubis, but I have adjusted now to the characteristics for temperature, print speed, and retraction distance so I'm using it very reliably. (I also had quite a bit of difficulty with a slight offset inside the E3D, where the bore of the aluminum body was not absolutely perfectly aligned with the bore of the threaded steel "heat break" tube that connects to the heater and nozzle block, thus creating a "ridge" that snagged the teeth marks. I finally solved that by finding the precise rotation angle of the threaded tube where the "ridge" was opposite the side with the teeth marks.)
I remember Plexus saying he really liked the E3D because "it just works," but for me it was a learning curve. I guess if you could put two machines side-by-side, with each one thoroughly "tuned up" for the particular extruder, you might find some quantifiable differences, such as maximum print speed or print quality - but I think the differences would not be huge. So bottom line, my personal take on it is that there's no overwhelming reason to choose either one over the other. They're both good. But I caution you, that's just my opinion; I am sure others disagree.
Printrbot Plus operational January 2013
Brass threaded rods (5/16" X 18) & nuts for Z axis
GT2 belts & pulleys
Cable chain to reduce probability of fatigue failure in wires
E3D V5 Hot End, 0.4mm nozzle, also 0.8 and 0.25 in use occasionally
PB fan mount + 40mm fan -- using printed mount adapter, not the E3D supplied fan
Injection molded extruder gears
Optical Z "endstop" (custom designed and built)
Have used many pounds of T-Glase filament. Now also doing some work with Ninjaflex SemiFlex
Print on glass with Scotch Craft Stick or other glue stick