Other than the adjuster and cam styles the arms look the same. The Parts on the 538's appear to be plastic while the bits on the 539 appear to be metal. And the 539's are lower in price. Hell, I say buy TWO sets...
Note that these brakes are intended for frames that use recessed tube style nuts. So if you don't have that feature on your frame's rear bridge then these aren't the brakes for you. The fork isn't a big deal since it can easily be drilled to accept the recessed style nuts. But at the rear it's a different story. You can still do it but it's a bit more work. And if you do kee in mind that you still need a saddle washer that is drilled out as well to aoid crushing the bridge tube.