SDL won't be able to do everything - like pixel shaders, because pixel shaders run entirely in hardware so require a hardware accelerated engine. The SDL runtime acts as a software renderer, which is slower but means your game can run even on computers without DirectX 9, which could be useful for lo-fi games aimed at the casual gaming market.
And yes, in future we could move on to OpenGL-SDL runtime, which could potentially do everything the DirectX runtime does (including shaders) but work on other platforms <img src="{SMILIES_PATH}/icon_smile.gif" alt=":)" title="Smile" />