"This change in our version numbering won’t have a huge impact on our players," says Mojang. "We are, however, hoping it’ll make it easier for our creator partners and modders to understand which of our version numbers represent a game drop, and which of them represent patches or bug fixes to our drops."
I know that Mojang is not being honest, that there's something going on, but I can't exactly pinpoint what.
The old numbering system is not hard to understand. It's simply 1.A.B, where A = major version ("game drop") and B = patch/bugfix. And the newer one is not easier, it's A₁.A₂.B where A₁ = year and A₂ = major version within that year.
Perhaps this is meddling from the above? It's possible Microsoft is trying to kill the Java version, but before that it's trying to leave explicit that all Java versions became "deprecated" - and having the release year in it is a good way to show it. But that's just me guessing.