Thompson is objectively the more deadly guy on the feet (greater percentage of (T)KO wins, more accurate, and more strikes landed per minute, to name a few metrics). Thompson has 12 wins at the moment, nearly 60% of them via (T)KO. His most recent win was a (T)KO of a former world champion that had never been finished in his career; Anthony doesn't have a single striking finish anywhere near that caliber.
Pettis first 12 wins saw him against much lesser competition and he was only able to pull a 41% (T)KO rate, a rate that has since dropped several percentage points.