Might seem like a strange question, but with everything going on in the manga is seems like some things in the manga have been a little rash.
The ship being sunk by Kaku. Seriously, this really annoys me. ALL of the Straw Hats stuff is gone. All of Nami's maps and navigation logs. All the stuff they collected from other places such as the tangerine trees, EVERYTHING. It just seems like that really should not have been done. It just seems like all of Nami's maps being gone is going to have a pretty big effect on the plot.
And about them fighting CP9. I think Oda probably should have thought this through a little bit more. One Piece is going to be completely differant after this. It will be hard to have any more "fun" arcs such as Davy Back Fight because it seems like marines will be after them constantly. Seriously, if they manage to beat CP9 And acually escape Enies Lobby, I mean, GEEZ! Its just to insane to think about. They will be known worldwide and all of their bountys will go up 10 fold. Its insane. And if they do defeat CP9, then what? Are they just going to walk out of Eneis Lobby (when they have no way to leave), Go back to Water 7, have everyone be all happy, get a new ship and just leave? I don't think that will be able to happen.
And that Gear 2 thing kind of annoys me. It seems like Luffy just got way to powerful and this is the start of where the OP charecters start the path to Dragonball Z.
Of course I still love the series. I just hope that this arc wont be the start of One Piece getting bad.