Well, you're probably battling more than just rough trails. Warm, muddy conditions will literally cause shoots to fall apart if they aren't given a chance to thoroughly dry between uses.
So you might consider getting TWO pairs of shoes. Not real expensive ones—there isn't all that much difference between mid-range and high-end shoes. But you can let one pair rest and dry out for a day while the other is on the trail. You might actually get more wear out of them this way than if you bought a pair, wore it out, then bought another pair.
For instance, you could get two pairs of Merrell Excel Grid trail runners ($90). These have air cushioning in the heel, grippy outsoles for good traction, water-resistant uppers, and a design that's best for runners with a "neutral" gait. That actually can help the shoe adapt to rough terrain more easily. The New Balance MX 841s ($80) are another reasonably priced trail runner. They're good for wet trails, and have New Balance's proven C-Cap midsole cushion. And, they come in widths, which can be useful. Lastly, Asics' Gel-Kahana 4 ($75) utilizes Asics' proven gel cushioning—long my favorite—in a tough, stable shoe.
Whatever you do, be sure to keep the shoes clean. Every few runs, hose them off and scrub with a light brush if needed. Take out the insole so everything can dry. That should remove the mud that harbors mildew, and rinses out corrosive sweat.
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