Assuming Malignaggi went to war with JLC, I have Prime Castillo over Paulie in a more convincing fashion than Cotto beat him. And I'm a big Paulie fan. However I think if he lost to JLC when he lost to cotto... and was fighting Cotto now, I think Paulie would win (he wouldn't be coaxed into the war he was because of his JLC experience)
Paulie would never beat Cotto he fought a weight drained Cotto and received a beatdown and only won 3 rounds at best, Castillo would beat him the same way.