I thought Saulo was Luffy's grandfather, and there'd be some kind of big ordeal about that between Luffy, Robin, and Aokiji that revealed a ton of plot.
I also thought Thriller Bark was a floating amusement park :(
I thought that Kaku would fight with throwing knives (at deadly accuracy) to live up to his "Mountain Wind" nickname, and probably fight against Usopp/Sogeking.
I thought Kaku was secretly a good guy in CP9 and would aid the Mugiwaras in getting Robin back, and so forth.
I thought Spandam would die a bloody, bloody death.
I thought Paulie had eaten a Rope Rope fruit :P
I also thought Robin was actually going to be a villain in the Water 7 arc.
For some reason, I had this idea that Vivi was going to suddenly have some super uber fighting skill of some sort, and jump off the shore and land on the ship when the rest of the crew showed her their X marks… =_=; Not what I wanted, really, but I had a feeling it was going to happen.
I thought Blueno was completely and utterly insignificant.
I thought they were going to reveal the name of the Ancient Country to be Raftel...
I thought that Sanji was going to keep up his "Mr. Prince" act for the rest of One Piece.
I thought that Sogeking was some old creepy man disguising himself as Usopp before I'd caught up... XD;
I'm sure there was a lot more, but I don't remember it all!