Knightquest
I take your point about the strongest and the fittest getting to breed. However, a good stockman will always ensure that he is breeding from the best available to him and, if he is ruthless in his disposal (by culling or distribution) of his less than acceptable products, he should always have first class individuals from which to choose his brood stock.
The problems start when indiscriminate or ill-informed breeders get carried away with creating fads rather than useful qualities and properties in their stock.
Gene pools can be naturally restricted owing to geographical influence; for example, where populations of wild animals are isolated from others of their species. This has happened in parts of Africa where some prides of lions are showing signs of hereditary weaknesses, and are desperately in need of an outcross.
Outcrossing is one of the problems encountered in poultry breeding where a strain of birds has been line-bred for a long period. There comes a time, when the stock is beginning to degenerate in some way(s) owing to the length of time without an outcross. The sourcing of the outcross is, however, dependant on finding an individual which is as good as the line-bred stock, and which will compliment that stock.
Crossing out into related stock is one of the best ways to lessen the possible detrimental impact of an outcross. This is why some advocates of line-breeding will always have two or three (preferably) similar populations of basically related stock; that is, relatives with common ancestors, from which the breeder can draw an individual which has some genes in common with the stock to be outcrossed. By that means, an outcross can be used to infuse vigour and strengthen characteristics in a strain.
Playing God is, unfortunately, practiced in many breeding circles these days, not least in domestic pets. Playing God is, however, in some breeding, essential if the world is to be fed.