A significant pro of separates systems is if you're doing more with your system than simply setting it up in your lounge to play CDs or vinyl, you can do a lot more than you can with a system. My system has an DAC with two CD players connected to it (one single and one 5 disc changer), along with two different computers: my home PC and my work. It also has a USB phono stage so I can record vinyl to my PC. The phono stage also has its own headphone amp inserted into the chain, (the DAC already has a headphone output). I also have a second amp that connects to my home PC, so I can run the home PC through either of two sets of speakers, depending on whether I'm playing a game and want vinyl on at the same time or whether I want to use the PC as a music source.
I don't expect anyone to have clearly understood all that, but the point is that a system would never have allowed me all of that functionality in one box and I'd have ended up with multiple systems daisy-chained together to achieve the same effect.
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