They are, without a doubt, theoretically better. And they can probably be shown to be better in practice, as well. The main thing going for separates is that not everything needs to be crammed into one reasonably-sized box, but can be split across multuple physically separate boxes. One benefit of this is that you can really isolate the power side of your equipment from the audio processing side and reduce possible intference, among other things. As a product designer, you can also splurge on larger, more expensive parts that just would fit into integrated equipment like your average receiver.
In reality, however, it is pretty much impossible to reliably tell the difference between separates and integrated components when compared in a double-blind tests.
