I understand and respect the choice of doing so, but my feeling is still saying that the Java version is the original, "real" Minecraft and the pocket editions are branches of it. Even if the pocket editions are played much more and are getting more and more love, it feels just weird that the Java version with this subtitle looks now more like a branch off then the other way around. Especially also because the Java version has still by far the most features and the most freedom and flexibility qua mods, skins and resource packs.
I think it would have been a different story if the pocket edition also had recieved a subtitle, namely just "Pocket Edition." It would feel much more equal to me then this.