I think the problem with going fully "designed" is that the design will be very fragile, because of how poorly we can model complex systems. The wonderful thing about the ecosystem is how resilient it is to problems... species diversity and genetic diversity within a species counteracts most potential problems. No matter how much suffering is caused by the natural state of things, it's better than having a designed ecosystem with minimal suffering that breaks when some pollutant or natural event kills a link in the carefully designed chain.