PCI-E has had the same standard since its inception: 1.0, 2.0, 3.0, etc. USB has changed multiple times and has remained confusing for the vast majority of people. What was 3.0 is now not 3.0. Even 3.1 has changed. There is no reason to use this naming convention they currently have but for some reason they stick with it..
Possibly they stick with it because it's usable (ish) and it was driving everyone up the wall when they'd change it?
PCIe also had things like "1.1", "2.1" and "3.1" - that fixed issues and added functionality - but there wasn't the same crossover between "feature sets and spec revisions" and "speeds" we see in USB today.