Both jackets happen to be very good. The Windstopper is cut a little larger so you can layer underneath it I actually find it warmer than the G50. It has pit-zips which should not be underestimated. Since it is a fleece exterior, it will absorb water (even with dwr) but....windstopper (the membrane in-between) is highly water resistant. The g50 is more of a classic soft-shell. The body is cut to the waist (ie...right at the belt line, so not that long). Conduit is probably more water resistant/proof than the windstopper. The exterior, being nylon or something with a dwr, will shed the water better.
Both jackets are durable, but if you plan to be on rocks, abusing your jacket or in wet environments, then go the G50. If you are looking for more of a hiking/backpacking jacket, warm mid-layer under a hard-shell or casual jacket, go with the Windstopper. Mind you, both are very capable jackets.
If you're still undecided, order the g50, try them both, and eat the 6.99 return shipping fee. Small price for peace of mind.