PCIe is obviously faster on paper, but there are a number of other considerations. First and Foremost is if your mobo can boot over PCIe (not all can). Secondly, are there any other bottlenecks in your system which would negate the savings you'd get from a PCIe drive, such as slow ram timings, finicky clock settings on your CPU/thermal throttle, etc.
And of course, bang for the buck. Right now PCIe 3 is not SUBSTANTIALLY faster than SATA, because they're both still relying on the same nvram chips and AHCI controllers at all other stages than the interface. Now once new tech like NVMe that moves data with less overhead becomes more standardized at the consumer level, switching to a PCIe drive would give you a bigger boost, by more efficiently making use of all the bandwidth space on the PCIe channel. And PCIe drives only really give a big performance gain in situations where you're constantly moving data onto and off of them, such as server activities. Things like games, which live in resident memory, will launch faster, but the actual game play between an SATA and a PCIe interface isn't likely to show any difference because they're not actively accessing the drive a lot.
so unless you're into spending bucks to say you have a part, or you REALLY want to future-proof your rig, I'd say stick with the proven SATA tech for now. Or perhaps take the money you would spend on the PCIe drive and instead spend it on a newer board with an M.2 slot to split the difference. that way you're getting most or all of the speed of PCIe, but not losing a slot.