badlogic, There was a thread in the cocos2d-x forums about stencil clipping being a problem and not being able to do easy batch rendering. I mentioned there that you guys are also struggling with it and improvements might be needed. Maybe nite from the cocos2d-x forums (or another cocos2d-x dev can help you guys with the stencil batching, or even fix it in cocos2d-x, so you'll have an easier live implementing it:
http://discuss.cocos2d-x.org/t/reduce-clippingrectanglenode-draw-calls/35143/7