@Jabra:
The CP9 already had a 5 year timeskip and made good use of it:
http://www.mangareader.net/103-2486-6/one-piece/chapter-379.html
I don't see why they wouldn't increase their skills during the 2yts.
Especially Kaku and Kalifa have loads of potential, when we consider that they consumed their devil fruits only a few hours before their battles. Hell, Kaku invented and named his attacks during his fight with Zoro.
As for the CP9 vs. Pacifista thing, I think we all agree that the power levels were severely messed up in that arc. Luffy getting a random super power boost, seemingly out of nowhere (no buildup etc), is only one example.
And then we have VA Doberman commenting on Lucci's power
http://www.mangareader.net/103-2529-4/one-piece/chapter-422.html
& Kuma commenting that Lucci loosing a fight was unbelievable.
http://www.mangareader.net/103-2581-13/one-piece/chapter-474.html
Maybe Oda gets things right should he reintroduce him. He didn't really live up to his fame and hype. (considering that an army of super powerful robots was introduced just one arc later)
Well Lucci dominated his fight with Luffy,i personaly think that he was defeated because he was gotten by suprise turning arround and finding out that Luffy was still breathing after a 3rd powerful Roukogan ,that and getting a Jet Gatling to the face and being Knocked Out but that aside it was still clear that Luffy had more damage done to him then Lucci i mean Luffy was half dead even Usopp stated it,that was like the fight where Luffy had to push himself further and further and overcome all odds for his crew sake and his. (What i said about Lucci applies to Crocodile aswell)
PS:Luffy didnt power boost out of nowhere he said that after he met Aokiji he had to get stronger so he had to train and think of a new way to protect his nakama and well he did have to protect them in this arc so yup :D