I dunno. Never had error or fail to format issues till I moved to Sierra last summer. I had bought a couple Seagate externals then and Sierra wouldn't format. They would on my older Macbook with Snow Leopard.
But I had to find out why. So I found others with this issue and what their solution was. I had to use my windows laptop and go in the terminal and type some things regarding something called 'diskpart1' in order to apparently delete that little bit of hidden partition.....think its the EFI partition that I guess is put on there since new disks out of the factory are FAT32 or exFAT formatted.....and once I did that I was able to format to Mac on Sierra OS.
In my search for solutions, I have come across on some developers forum, such a thing as USB being problematic since El Capitan or Yosemite showed up. I wouldn't be surprised really. I don't put it past Apple to turn users off USB and therefore to Thunderbolt. Then of course, once everyone hypothetically adopts TB as a standard, Apple will then abandon that for something else, lol
So you have 3 issues here.
First - the USB (your original) issue. So, for me, on my 2014 Mini, I have a EyeTV (USB2) recorder, a USB3 powered hub, a keyboard switch and a video switch (only takes power from hub). On my USB3 hub, I have, at various times, a DAC (USB2), a software license dongle, various external HDD's - almost all USB3, a couple of USB3 HDD docking devices (mentioned earlier), a couple of iPads, some flash drives - USB2 and USB3. So I have a fair amount of variety in what I connect. Obviously not the same as what you have, but probably more than the average user.
As mentioned earlier, I have observed the port-order issue on my 2014 Mini, which I mentioned earlier, I believe, is the result of some power issue between the USB devices connected to the Mini. By the time the USB data from the external ports come to the CPU in the 2012 or 2014 Mini, it comes over a single bus and there is no discrimination in terms of port order.
On my 2012 Mini, I don't have the same variety of devices and I still run El Capitan there. I haven't noticed the port-order problem there. Unlike the 2014 Mini, I'll mixup which device goes into which port and I still don't notice an issue.
I have observed differences in how my HDD docking devices work over the different OS's. On my 2014 Mini I have had El Capitan, Sierra and just recently High Sierra. I didn't notice any uptick in problems going from El Capitan to Sierra. And in general, my USB devices worked without problems on Sierra.
It's possible you have a hardware issue on the Mini and maybe you should take a trip to an Apple store and have them check your Mini out. But my guess is that you probably you're probably just going to need to troubleshoot. It would help if you have another computer (having Windows would be helpful) to make sure it's not the USB device that's the problem. A different hub (powered would be best) and perhaps not mixing USB2 and USB3 hubs may help. USB3 problems are not unusual as perhaps the specification is not clear or vendors are not implementing it fully - those are my guesses.
As for formatting in Sierra, people do report that formatting will fail but usually works on the second try. I have that experience more often than not. I don't think having the EFI partition is a problem for disks that are going to be used on a Mac. If you format a completely clean disk in Sierra, I think it will put the EFI partition there. All of my disks (except the APFS disks) have EFI partitions and I haven't had to delete them to get the disk properly partitioned.
I don't think Apple is creating problems in USB to promote Thunderbolt. They address different needs. Apple will not abandon USB in the foreseeable future. If anything, if Apple goes ARM for it's Macs, they might decide to abandon Thunderbolt and come up with their own proprietary "standard". The problem there, of course, is that they would have to build a user and device base.
EDIT: I'm still getting familiar with APFS and it turns out the EFI partition doesn't exist on the "synthesized" disk but it's still there on the "real" disk. One of the SSD's (PCIe NVME) can't be formatted by any macOS other than High Sierra, so it was High Sierra that put it there.
