Why not replace the human genome with it's decoy genome version?
To clarify, when you say "decoy genome" you hopefully mean the decoy genome and the reference genome together; the decoy genome itself is not a complete reference, but a collection of contigs assembled from reads that didn't map to the current reference genome, but are known to be human sequence.

The decoy genome certainly seems to be a useful supplementary data set for speeding up read mapping to the human genome but it cannot be better than the reference because it is not comparable to the reference.