Dangerous generalization: an omni is flatter and more accurate, in terms of exactly reproducing the source.
Of course, the reason that's dangerous is because there are an enormous number of omnidirectional mics in the world, and many of them are colored either by design or due to not really caring to make an accurate mic.
The reason the generalization is at least somewhat true is that the things you have to do to a mic to make it directional will also tend to produce anomolies in its frequency response which may vary depending on the source and its location (most obviously, the nearly universal proximity effect). If your goal in making a mic is to make it ultra-flat (like, say, if you were making an intrumentation/measurement/test mic), you'd probably use an omni design.
