Separates are more tweekable. Every separate component I have in my main system that is included with a receiver is a different brand. Did not start out this way, but by swapping different things over time. This includes things like trying different cables links between components.
A smaller system in my den/home office has an integrated amp. The rest are separates. More of a space issue and its good enough as is.
My HT system in the family room has a HT receiver (Onkyo). The only separate is the DVD player (there are receivers where this is built-in also). This was done because it is good enough for me for movies, the rest of the family likes it, and it is easy for them to use. They are not into gadgets and just want to plug and play.
So I guess I believe in separates where the sound is the most important thing. I will compromise for convenience.