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Pokemon are also pets.
People breed pets till they think they're perfect and usually sell them or raise them.I don't see anything wrong with that.
Also natures,IV's and EV's help make your Pokemon seem more unique, granted most people are probably going to have the same thing since a lot of people run the same sets in competitive, it does make your Pokemon seem more like an individual. hence IV's
Personally the only thing I hate is the lack of events we get each gen.Gen 4 had a lot and I loved that so much. Also I hate that they take away amazing aspects of the game like contests that dance hall and pokeathlon. If all those appeared in X/Y it would have been my favorite game.