The only difference is that using the secondary lets you "touch" the beer before it goes into the bottle.
Putting it straight into the bottle, you can't do anything with it until it hits the glass.
So, if you want to do anything like post-ferment dry hopping or using oak or anything, you have to do it in a secondary. More commonly, it's just a method to let a little additional sediment settle out. So, most people just do it for clarification. I've never left a beer in secondary for over 2 weeks but I'm looking at doing something with oak soon, so I'll need a longer secondary time with that.
EDIT: Maybe there's an effect on aging while its still uncarbonated?