It seems you are buying a used machine, perhaps on an auction site like EBAY? That would explain the older OS, flickering graphics and perhaps even slow SSD. That would also explain why the Mac Pro was somewhat affordable for you, since buying new would surely cost much more than what you paid.
Curious if Apple will release a new Mac Pro this year. The one you have came out in 2013. Regardless, it still will not be as affordable as the iMac. But at least with the latest hardware, someone out there might be able to justify the high price of keeping electronics cool. For now, my SkyLake iMac at the office is running fine at 39°C most of the time. The fan runs at 1200rpm, which is faster than the 700rpm of the Mac Pro, but I cannot heard the iMac's fan at 1200rpm. And the 5K screen is drop dead gorgeous.
The only other thing I will add is that Intel is up against a wall on CPU development. I've been using Macs since the 128k in 1984 and I can tell you that the huge leaps in CPU performance we'd see almost every year in the past are now gone. SkyLake runs cooler that prior chips, but performance is the same or worse than Broadwell. And upcoming CPUs look to be just as lackluster. It's questionable whether Apple will ever run Macs on its A-series chips, but even then we reasonable cannot expect them to best Intel, unless Apple rewrites code specific to A-class chips in something like Assembly Language (which isn't going to happen, even though that's what Apple did in the early days of the Mac). No, performance will probably only keep trucking along with more advanced GPUs and GPU-accelerated code. Very few companies are taking advantage of that now. If more companies, Apple included, took full advantage of GPU power, the Mac Pro should easily trounce the iMac in most tests. But as it stands now, the iMac trounces the "Pro."
Anyway, I hope you get the SSD troubles sorted out. The speeds you posted are not "slow" in terms of spinning platter hard drives, but they are slow relative to your earlier Mac Pro and especially slow compared to the Skylake iMac.
Best wishes.
