I'm not a hater yet I think there's some truth to that complaint. The old MP could hold internally most of what you want. The nMP cannot.
You have to now use a rack and take up office (or closet) space to hold the external drives because the nMP does not have the expansion bays. Additionally if you had an old MP, and everything set up with internal drives, you'll have to buy external drives which adds to the cost.
I've said this before, if I had the $$, I'd buy one, I love the design and yes it would be overkill for me. Since I don't need it, and I don't have the money for it, I'll not be buying it, but I really do love the design. That doesn't mean I'm willing to sweep some of the short comings under the rug
The argument is artificial, here's a real world use case.
I have three sit-stand desks with a computer setup on each. One a Windows laptop for work, two is a Mac Mini for email and such, and three is my workstation with a 2009 MP. The MP has to sit on the floor as it weighs over 50 lbs probably, and therefore it's got a perfect MESS of cables going to it. And it has a few external boxes, eSATA 8 bay hard drive for one. By far it's the messiest desk of the three, which is distressing to me as a clean desk helps me think and work better.
Now I moved it into another room for another use, and while my nMP isn't here yet I set the desk up with everything except it. I'm down to four clean external cables, power, two ethernet and one TB off to the peripherals. Since it's on the desk all the keyboard, mice and display connectors are
contained on the desk, instead of dangling down to the floor with the oMP. I wish I had pictures but it's about an order of magnitude more contained. If I wanted to I could bring it down to two cables, by putting the ethernet off the TB chain. And I'll be adding external boxes, but they are off in a nice cabinet, very clean and tidy.
Two points, the oMP did not contain most of what I wanted. It contained some of it. And two, due to the ginormous size, it has to be off the desk on the floor with a desk to computer cable clutter that I couldn't find a way to organize in 5 years. So in this real world example I've proven that the nMP can easily be less cluttered than the oMP.
Can the oMP be less cluttered? Yes, if you put it on your desk behind your monitor, and only have internal peripherals. However few people would want that there, or would have a desk that could take it either in size or weight. I'll also note that in that configuration you'll have a big looming computer staring at you, and the noise would be quite louder than when its on the floor. Clearly the computer was meant for the floor, which is why Apple included the big handles and equivalent feet.
EDIT: Here's a video from Corning on the technology
http://www.electronista.com/article....to.100.meters.tested.10x.longer.than.copper/
You can have all your Mac Pro peripherals in a different room. Or have the nMP in a different room and just your monitors (with included IO hubs) on your desk.