Are there any "problems" with the ToE that are generally not addressed?

Hello, first post. I heard this argument somewhere in my debates and was wondering. Breeders and scientists have bred many animals to a very high degree, as in, beyond what natural selection would produce. For instance, rock pigeons with such large breast muscles and feathers that they are physically incapable of flying and are only kept alive because they are cared for by human aid. The point of the illustration is this. Why do animal breeders hit an "invisible barrier" when breeding animals where they do not change any more regardless of the specimens used. For another instance, feathers were mutated to such a high degree that the rachis was gigantic and the barbs no longer interlocked, but that they could not get the mutation to go much farther than that point. The barbs fused in a few instances but not regularly, and the feather still remained a feather. Should we not be able to scientifically breed animals backwards to prove evolution?

I do not need a horse changing to a cow, just a horse changing back to his anscestors. Surely the genetic material from earlier evolution should still be in the horse now. Sometimes I've heard that recessive genes come out and a horse is born with three toes. Should not other genes exist, and allow us to breed it backwards?