I think the Winnebago will be better quality. I looked at a lot of RVs when we were shopping, and the Winnebagos were designed and built significantly better than the Thors. They also have a fiberglass roof instead of rubber, so less likely to have future issues and less maintenance.
We preferred the interior design and look of the Thor, compared to the dated campy look in the Winnebago, which is why we got a Thor, but as far as quality I think Winnebago is better.
We bought ours new, but I think getting a 2-3 year old RV might be a better way to go. The initial bugs should be worked out, and the huge initial depreciation has already happened.
Good luck with whatever choice you make!
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