I'm not terribly familiar with how the Spine runtime works. I know the newer versions do skinned meshes, I assume that is what you are talking about? I'm going to make even more guesses that the mesh skinning has to be done on the CPU and that is probably more expensive than draw calls.
When trying to solve performance problems always use the tools before guessing. The easiest place to start is the FPS gauge in Xcode. It should always show up whenever you run a program on a device. Click on it for more information:
The green bars on the far right are the most important. It gives you an idea of if you are CPU or GPU limited. Draw calls cost basically nothing on the GPU itself, so if you are GPU limited, it's because you are drawing too many pixels. Reduce the number of pixels drawn by drawing smaller or fewer sprites, cut down on particle effects, or full screen layers. If you are CPU limited, you need to run the time profiler instrument to find out more information. It gives you a nice detailed breakdown of where all your CPU time is spent. Then you don't have to guess what to optimize.
FYI: You are correct that the iPad 3 usually has the worst performance of all iOS devices for games. It has a GPU that is ~2x as powerful as an iPad 2, but with 4x as many pixels to draw. It puts a lot of stress on that GPU bar. I think the CPU speed is the same as the iPad 2 as well.