Just to clarify, Dolphin's specialized shaders simulate fixed-function blending/texturing too. What's different about ubershaders is that a single shader can handle a wide variety of fixed-function states whereas a specialized shader can only handle a single state.

Thus whereas specialized shaders have to be generated and compiled on-the-fly resulting in stutter; ubershaders can all be pre-compiled before running the game. Add to this the capability to asynchronously compile specialized shaders to replace ubershaders and the performance loss of ubershaders becomes negligible. A rare case of having your cake and eating it too.