Thats a difficult one, for me, these are two different fabrics for two different uses. Goretex is great for heavy rain in warm conditions or if you are being active or travelling light. It is very breathable and there is such a vast array of features, colours and designs that it really is difficult to make a choice. On the downside, it isn't the most hardwearing, dirt and age effect its breathability. The sightest spark in the wrong place can render it useless. It isn't the quietest of fabrics (not good for hunting or wildlife watching). In extreme temperatures (cold and heat), it can become more of a liability than it's worth.
Now then, waxed cotton, is warmer and very hardwearing. it ages well and its water repelency can be renewed as often as needed. It is far more resitant to fire and dirt (it can just be wiped clean).The designs, whilst not as varied as the goretex jackets, do seem to be more suitable for the rough and tumble of bushcraft, hunting and general use. They are less fashionable but more timeless.
But, it is heavy and can be too hot in warmer weather or whilst being active. For a good make it can be expensive and any damage can be pricey to repair. Many of the designs have weak spots that allow water to penetrate in heavy rain.
So there you go, a brief rundown of pros and cons of each. Hope it helps you in what you need. I've got an expensive goretex jacket, a triple point jacket, 2 wax jackets and now a ventile jacket. Depending on where i am or what i'm doing, dictates what jacket, although, wax and ventile seem to be the favorites.
(at the end of day its swmbo who dictates what new jacket i buy
Good luck
Baggins