I own both, and the JP2 is newer in my collection, but I'm finding myself playing JP2 over and over, and hardly playing the POTC these days. Main difference is the combos on JP2 are so satisfying and there's a relative lack of combos on Pirates. Pull off a 5 combo on JP2 where you're picking off 4-5 rescues in a row and it's just amazing. I still haven't beaten all 3 control room modes, or all 4 trex modes, or reached visitors center (although getting close now, had 19 rescues today!), but I'm rapidly improving on it so it's more addictive at the moment.
Also, watching Karl throw up a 31 million shot on pirates almost ruins pirates for me ;p