Here is one of the main reasons I like Enies Lobby Arc the best.
Straw Hats are Pirates. And they are finally fighting the Government who is against Pirates. While we look at the Government as being bad guys, essentially the Government are the good guys, and the pirates are the bad guys.
And our Pirates, the StrawHats declared WAR on the WORLD GOVERNMENT. Thats a BIG thing to me. They'll literally be known throughout the world, and be at war with the government.
Crocodile was a villian, yes. But Crocodile was more or less a Pirate, still. He had a bigger plan than the typical pirate, but he still is more like a Pirate than Luffy was. So while we look at Crocodile as a big time villian, I simply look at him as a typical pirate with a bigger ambition than the sea and looting treasure. So it was like a Real Pirate Versus Luffy, a Pirate who isn't a typical pirate. He is more of a Marine, if anything. Strawhats rarely do anything bad/break the law, and they defeat Pirates and people who would cause harm to the world like the Marines should.
People compare Lucci and Crocodile… But you can't. Lucci is supposed to be a good guy. He is part of an organization of the Government who does underhanded things. But he is still doing what he is doing for the World Government. That protects the people. Lucci has no real evil ambitions. He is simply a strong fighter, protecting the World Government.
So when you look at the enemies of the arcs. Don't look at Lucci being the enemy of this arc. Look at the entire World Government being the enemy for this arc. Lucci is simply the strongest atm, fighter that the World Government has to offer. But it is still War against the World Government. Not War against CP9/Lucci.