Yes Spine 2.x and Spine 3.x are extremely different.
Yes, v2 and v3 in spine-cocos2d-iphone refer to cocos2d v2 and v3 respectively.
The current Spine 3.6 branch is for cocos2d v3. Backporting the non-rendering parts should be trivial. However, the rendering part has been completely rewritten, relying on some stuff only available in cocos2d v3. Plus we had to add our own low-level OpenGL ES rendering code to support tint black. I'm not sure if cocos2d v2 supports that.