There are many difference, even down to some artstyle choices. The anime is produced on the "cheap" and, so Oda's style doesn't transcend well.
The series is guilty of low frame rates, lack of animated scenes (part because it draws out manga scenes and part because having 2 people standing around talking is cheap animation), and a lot of off-modelling depending on who is the artist. I mean the Ace versus Blackbeard fight... It was kinda badly done. The worst animations if I had to put a finger on it would be the Whitebeard war arc, a LOT of scenes were really cheaply done in scenes that should have been epic.
Its not the manga is perfect, as Oda has produced pages that are a cluster-**** to read at first glance and he does take corners. The best example would be the female body types, for many arcs Oda restricted himself because he couldn't draw women well unless it was a "8" figure. So a lot of women shared Nami's body typing. He still prefers that... But... Miss Monday would likely be the first woman that started it all as Oda became aware just before the BW arc that he was getting criticism over his depiction of women. He has tried to fix this, as people have pointed out this can be both a negative thing to portray all women like that and because not everyone finds the figure 8 body attractive. By the time you get to Amazon Lily... Its clear his worked things out, though he still will rely on the "8" body for characters he draws a lot.
Sometimes the anime actually does things better then the manga... I personally think the Bon Kurei and Sanji fight is better in the anime then the manga. But a lot of times... Eh... The way the anime is can make a scene boring that was great in the manga, so I tend to think the tedious nature of the anime makes the manga better. There are worst anime out there.... I mean I've watched animation thats suppose to be top end resort to noodle arming fight scenes so... Lowering your expectations is fine.