These days, if possible in the computer(and that's not really a question/problem in your build) I will always choose PCIe over SATA.
Most "cheap" SSDs these days will saturate a SATA III connection at least in sequential read(non-sequential read and all write operations are where drives start to show their differences).
If I were building...and for me the only thing I'd likely even "build" now would be another Mac Pro 5,1, I'd go with an Evo 970 NVMe drive in the largest size I could budget/afford(BTW, I know there's at least one other Mac Pro 5,1 user here-the latest firmware patch under macOS Mojave enabled full native support of NVMe).
With that said, I agree with others that you may have other issues if you Samsung Pro is slow. Yes, drives have improved in the last few years, but even low end SSDs still feel fairly fast to me in day-to-day use even when running at SATA II speeds. I'd make sure TRIM is operating properly, as that is one big thing that can really kill the performance of an SSD over time. I don't begin to know how to do it in Windows, but once you've made sure TRIM is enabled, there should be a way to do a mass force trim. In *nix systems, you generally boot into single user mode and run FSCK...I've worked on Macs where someone installed an SSD without enabling trim(it required a 3rd party tool for non-Apple SSDs up until very recently) and the drive had bogged down to worse than typical platter drive speeds. Enabling trim and then FSCKing it a few times brought the performance into line with where it should be.