Bah. I forgot about PVR textures. Cocos2D has always loaded textures upside down compared to OpenGL (and it's own) convention. This can make writing shaders and custom drawing code confusing. I figured v3.1 was probably the last chance to fix it before 4.0.
PVR files are going to be a problem though. Technically, the PVR files used with Cocos in the past have been upside down. OpenGl textures go bottom to top. Since regular image files usually go top to bottom, Imagination's PVR tools actually flip by default. (Apple's texturetool utility does not, nor does it provide the option -_- )
Uncompressed textures can be flipped easily enough when loading using GL's unpack alignment. PVRTC compressed texture could be flipped, but not trivially.
I'm a bit torn about what to do. Most PVR textures used with Cocos are probably made with Texture Packer so there is a trivial fix. If they are using Imagination's tools, then they would have had to tell it to disable the flipping. Easy fix again, just reenable the defaults. If they are using Apple's tools, they will need to flip their images by hand.