They probably did it because the Japanese don't have the word version in 99% of their games. Not only that, but the word version is extraneous; for example, "X" and "Y" already differentiate between the games.
If you want some logical/literal explanations, take the definition of version:
Version (Noun); a particular form of something differing in certain respects from an earlier form or other forms of the same type of thing.
By this definition, the only games that are versions are Blue (Japanese), Yellow, Crystal, Emerald, Platinum, Black 2, and White 2, because they are based off of the other games in their generation (Remakes like Fire Red/Leaf Green are remakes/remasters rather than versions of the games they are based off of). Therefore it is almost fitting that the last time there was a version game was also the last time the games were called versions at all.
Game Freak probably knew they were going to stray away from the Version trend (they almost never had it in the Japanese titles) because there technically wasn't versions, and the word version is extraneous and makes typing/writing/saying the games' names harder than it should be. :P
They are then, therefore, not versions of each other, but versions of their story. They weren't based off of a "first game", so they can't be versions of a first game if there is no first game to start off with. Despite their stories being based off of the same thing, the entire games aren't really versions of each other.
TL;DR: Since the last time a game was actually a version (Black 2/White 2) Was the last game that had version in it's title (and that the Japanese Titles only used the word "version" once), It makes sense to drop that part of the name. :P
Hope I helped!