Badass Decay: In the original, Mojo was one of Townsville's biggest threats. In his one, they downplayed it extremly, and turned him from a Not-So-Harmless Villain to an utterly Harmless Villain. Even the Girls saw Mojo Jojo as one of their toughest archenemies, here they don't even take him one bit seriously.
Broken Base: Fans of the original either like or despise this take on the Powerpuff Girls.
Miko Shirogane/Shirogane Z/Duchess Morbucks has gotten some fanboy attention too.
Foe Yay: Momoko/Blossom and Himeko/Princess. Episode 43 is a good example, showing them butting heads yet later showcasing that they still consider each other friends regardless (the real Foe Yay part comes at 06:26.)
Growing the Beard: For the first five episodes, Mojo Jojo was the villain, but wasn't much of a threat. Then episode six introduced Fuzzy Lumpkins, the first villain to actually give the girls a hard time, and Himeko/Princess Morbucks, whose take on the original character was very well-received. From then on, more villains began to show up and the show got better.
Woolseyism: For the Asian release (dubbed in English of course), Peach's name was changed to Poochie (thank goodness for that), the girls' secret identity and actual names are the same, and Mojo Jojo speaks in the same manner as his Western counterpart (no verbal tic of course).