@thomash @adamgeo. Cocos2D-Swift is still a stand alone API, and you can continue to develop games with it, without using SpriteBuilder.
The main difference is, that we now use SpriteBuilder to handle installing, updating and creating templates. This was a major PITA with previous versions, and the templates breaking with Xcode 6, was a good example of the grief created because of this.
So you really have all the choices.
You can just create the template in SpriteBuilder, close it and continue "the old fashioned way". You can do most of the programming in XCode, and just use SpriteBuilder for menus, or assist you with effects, or asset handling, or you can use SpriteBuilder 100% to develop your game.
And then SpriteBuilder of course gives you the option to build your game for Android also.
So while I understad your concern, we are in no way trying to force you to do anything in a specific way. We are just offering you more ways to do it.
About the versioning.
To keep track of which version of Cocos2D goes with SpriteBuilder, their revision is set to match. The overall release is 3.3, but bundled with SpriteBuilder 1.3.5, Cocos2D-Swift will be versioned 3.3.5.