The Team Rocket trio have definitely had their coolest moments in Unova, since that was when they got a complete change, becoming more professionel, less kidding around, and actually creating plans with much more likeliness to succeed, and best of all, no more freaking holes! But as has aready been mentioned, they're no longer the same characters.
They may bear the same names, bodies and ranks, but all that was actually Jessie, James and Meowth has been washed out by the demands of them being less annoying and acting more as villains, rather than just showing up and wasting the episodes. And for my opinion, I really hate it. They may not have been cool in the most prominent way, but they were kind of the comic relief characters of the series, as well as they acted as part villains - part protagonists. At times they would help Ash and friends, and if it weren't for them and their crazy ideas, a lot of things would've gone differently, as well as I felt like they were really likeable before. Now all that was of the original Team Rocket just seems to have been sucked out of them, and they just remain as empty shells of a trio set on pleasing their boss in every way possible. Except now they don't have their personalities to get in the way of that, and are more or less perfect. Pffffft.