Well there is an advantage to people no lifing breeding and hatching eggs, less crappy pokemon on wondertrade. Getting a good natured, 4 or 5 perfect IV'd pokemon instead of another freshly caught bidoof or flabebe is pretty awesome out of the blue.
Those whiny people who complain about PokeGen/PokeSav give the rest of us "legit" players a bad name. I don't care if you hack your Pokemon, as long as they're within the legal limit it's fine with me. I'd rather breed my own though, doesn't take that long anymore anyways. I bred an entire team in one day.