I was in the same predicament, going back and forth between a fully loaded Retina iMac and a 6-core new Mac Pro. In the end, I went with the nMP. Here was my thought process:
1. I use applications that regularly take advantage of higher core counts, as I'm an audio engineer. The nMP is (obviously) the only machine Apple sells with more than 4-cores, and as of right now, is the only headless Mac you can buy with a quad-core processor at all.
2. I like the idea of not having my computer fused with my display. This may not be a big deal to most people, but the display will greatly outlive the usefulness of the innards of the RiMac. Once the computer has aged and no longer meets your needs, you'll need to get rid of the screen as well, especially since Target Display Mode is not a thing that exists anymore.
3. Personal preference, but I find that having a 34-inch Ultrawide at 3440x1440 so much better than having a 4K or 5K display, for my needs. It's really hard to go back to 16:9 after using one of these for a couple of months, no matter the DPI.
4. My previous desktop machine was a 27-inch 2010 iMac. It was good to me for a couple of years, but the fact that it did not have a solid state boot drive made it quickly show its age. After the two year period, I needed to have it serviced three times (thankfully, I had AppleCare). Twice to replace the screen due to the 'LCD Contamination' issue, and another to replace the hard drive. Lugging that thing around a mall was a pain. This kind of turned me off to the iMac idea in general.
5. Even if I could overlook all of the drawbacks of an iMac and make do with the quad-core, the Retina iMac, I feel, was not ready for primetime. Its design doesn't serve the innards well, which now run hotter than ever. Yeah, the GPU was made to run at those temps, but what about everything else inside of the casing? I'm not convinced that damage due to excessive heat wouldn't happen in a few years time. Even if that didn't happen, the system has some hardcore throttling going on with the i7/295 combo, so when working for longer periods of time, the nMP will throttle down less (or not at all) due to the system staying remarkably cool overall. The 4790k is a sweet processor, but what's the point if it's just going to run hot and whittle itself down anyway?
5. The 5K screen is really really nice, but aside from looking sharp and crisp, it just doesn't serve much purpose in the grand scheme of things. The world is just now barely starting to latch onto 4K as a standard, and Windows (which is what most of the world computes on) doesn't even handle it all that well. I feel that while all of the extra pixels are nice to have, it doesn't serve much of a greater purpose.
So yeah, I went with the nMP, and aside from the coil whine issues which I'm dealing with, I love it. Would I have preferred it if the system had either two gaming grade GPUs or one gaming grade GPU and dual CPUs? Yeah. But, it is what it is, and it was the best option for me from what Apple offers currently.
Plus, while I went through some headaches with the retailer I ordered from, I ended up getting a fantastic deal on the system config I ended up with (6-core stock, AppleCare, and a brand new 1TB PCIe SSD from an Amazon seller).
