Well, since it's a matter of personal opinion, I hope I won't be flamed by this. ;)
The first thing I remember not being very fond of in the story was God Enel. But then I saw he was the first from many enemies I HATED because wouldn't put up a real fight. Even as logically acceptable as that is, I ended getting annoyed by those enemies who wouldn't face Luffy, but would use their abilities while running from him. I almost had the same feeling with Moria, for example.
Also, Enies Lobby was kind of disappointing for me. If I can put this in words, I believe that is because I liked Water 7 VERY much. Really, really, it's one of my favourite parts in the story up to now. But when the actual expected fights began, they weren't so… I don't know, epic, as Arlong, or Crocodile have been before them (again, IMO). I liked the idea of the exchanged fights, liked Nami vs Califa and Sanji vs Jabra, and Robin's "I want to live" scene. But Franky vs Fukuro was booooring, Chopper's only got interesting because of the Monster Point (and only by itself, not the fight), I got REALLY annoyed that Zoro had the most ridiculous opponent ever (not to mention that he finished the fight with one of the moves I hate the most for sheer lack of an acceptable explanation). And Lucci, meh... one of the less charismatic main enemies of the series up to this point. I only managed to like a liiiitle bit more when I saw the end of the fight animated (the Jet Gatling got AWESOME in the anime)...but while I was reading the manga, I was praying to Gan Fall that could finish at once. Bruno's fight was MUCH cooler that Lucci's. Again, and again, and again, in my humble opinion. ;)
Next! o/