One of the changes that happened between Cocos2d-x 2.1.5 and 2.2 was the removal of templates for projects in XCode (I do not know if project templates existed in VS, etc).
The new build system creates projects under the Cocos2d-x installation (at least on Mac) and that is where the project files appear to reference them. This makes it very difficult to move the project without hand tweaking. It also makes configuration management more painful, depending on how you set up your system (e.g. a root/tree like svn or a "drop it anywhere" like git).
Also, the Cocos2d-x library is built as that, a library. In previous incarnations, it was placed directly into the project. On one hand, if you don't alter the root library code, this makes good sense. On the other hand, if you occasionally tweak things for a specific project, you have altered all your projects that depend on it. Yin/Yang.
I'm still very positive on Cocos2d-x. I have not upgraded to 3.0 or 2.2 yet. When it matures a little more, I will switch over, regardless the changes. For what I need, I'm pretty sure it will still get the job done (well).