The mare I just bought has a lot of conformation faults. Her bloodlines all come from the Budweiser Clydesdales. Would I breed her? No. To me she is my treasure and my soul but I don't consider her as good enough to bring another unfortunate foal into this world.
I also have a Clyde/Qh cross. Her conformation is far better than the new filly I own. Her temper is 10 times of any horse I have ever met or known. If I were (ridiculous enough) to breed another mix match like her over a purebred of something else I would have another foal like her again.
A horse is a horse and whether or not people want to admit it, you have very sick animals being born every day regardless of whether or not they are purebred, registered etc.
I think the better horses out there are the ones that are bred with mixes as they become what people consider to be safer than a lot of the hot lines others will breed.