Jerry Coyne quotes Robert Ingersoll on the challenge that evolution is supposed to present to the belief that God is good. The idea is that a good God would create by fiat, just as recorded in Genesis, instead of using evolution, which depends upon animal carnivorousness to develop new species.
Now I agree with Ingersoll and Coyne that there is something wrong with animal carnivorousness (yes, it is tough on those fishes). But then, we have animals eating animals now, regardless of whether evolution happened. So the present existence of animal carnivorousness is a problem for those who believe there is something wrong with it, but also believe in a good God. Does evolution compound the problem? It means that carnivorousness has been around a lot longer than human beings, so that attributing its existence to a human "fall" isn't easy to do (though William Dembski tries it in his book, The End of Christianity). With C.S. Lewis, I prefer to blame Satan for the problem. I don't think Coyne will think much of that answer. But it works for me.
But Coyne implies that there is an additional problem that he calls "waste." Somehow it was a waste for God to use the process of evolution to develop new species. But it is only a waste if the animals involved in the process had no special value to God. Do we know that to be the case? Hardly. Jesus told us that God cares about each sparrow that falls to the ground. It seems very likely that God also cared about the individuals of each past species that ever lived on this planet, and that they were of value to God in and of themselves -- not just because they were also the means to future species. To God, all things, all animals, all people are ends in themselves, not just means to other ends.
So yes, the problem of human pain and suffering, along with the problem of animal pain and suffering remains, and there is no easy answer. But I think we can dispense with the notion that there is an additional problem of "waste."