Both systems are built to a very high quality, the WEPS uses injection-cast aluminum for most of its components as far as I can tell, and the EP uses either machined industrial polymer (EP Pro) or molded plastic of some kind (EP Apex). For the purposes intended, both serve quite well, and the processing is done to a very high standard.
I'd consider them equal in build quality, although WEPS has had some issues of late with manufacturing defects. They have identified and corrected those problems, it was an issue with one of their suppliers, but it's worth being cautious of if you purchase a used unit. There is, of course, no issue at ALL getting immediate response and replacements for the defective components from Clay, should you happen by some way to get one of the units with the soft jaw problem. Mine did not suffer from the defect, and has had no trouble in operation at all. As a matter of fact, Clay just sent me an upgraded set of guide rods that reduce play in the sharpening process even more for higher precision. I believe those represent a potential new process they're looking at for future improvement of the design.
The Chosera stones I purchased came from Ken at ChefKnivesToGo, he's a very easy to work with and helpful fellow. Tom at Jende also offers the Choseras, again a top-shelf guy to deal with. Shaptons are another good choice for upgraded stones, and I'm actually looking at a Shapton set from Tom right now to take my EP sharpening up another level.
EDIT: Incidentally, there is nothing at all wrong with the factory EP Boride stones, they work very well! The Shapton and Chosera stones just represent the pinnacle of manufactured abrasives at this point in time, and are an upgrade option for the real snob.

If you are just starting out, I would just get the stock set with the EP OEM stones up through 1K. Once you've mastered those, you can easily progress to adding additional stones to improve your sharpening yet more. Off the stock 1K, you're already (with proper technique) going to have an edge in your hand sharper than probably 95% of America has ever even SEEN, much less used. If you want to go whole-hog right from the get-go, CKTG offers their own "Custom Chosera" set, that has an EP Apex, and every Chosera stone you could possibly want. The price is actually quite reasonable for what you get.