Carefully chosen benchmark comparison
Classical simulated annealing is not a particularly good optimization technique which was acknowledged in the paper:
"It is often quipped that Simulated Annealing is only for the 'ignorant or desperate'."
There are much better classical optimization technique which would compare much more favourably but they used it because it was the closest analogue to quantum annealing.
Simulated annealing also doesn't do well with potential energy surface which contain deep, narrow wells where it can get trapped. Quantum annealing can tunnel very efficiently through them and so they chose a problem which suited it. From the paper:
"carefully crafted proof-of-principle problems with rugged energy landscapes that are dominated by large and tall barriers"