Well, I just wrote some shaders for Unity and this actually also showed me the ugly sides of the current system. My biggest problem at the moment are some very strange artifacts, that occour with any shader. Seems as if there is a pass rendered, I didn´t define in my "shader": http://forum.unity3d.com/viewtopic.php?t=56563
You can find some more information about the current shader system here: http://forum.unity3d.com/viewtopic.php?t=56396