The problem with a unified shader engine is that you may give up too much control. As great as unified systems are, games are still very much in the hands of the artists. Hand tweaking lights and how an effect reacts in different environments is important.
Take an ember of coal. In the sun you probably would not see the red. But if you stick it in a dark room not only can you see the red core through the cracks but you will also get a glow and some heat haze.
It is hard to imagine getting a unified system to understand the individual properties of thousands upon thousands of different items (things rarely react the same way to heat, tension, pressure, light, etc). So you are either looking at a really advanced properties system, very complex shaders with a lot of "if - then" type design, or you can just have an artist tweak the shaders for the different environments.
The last will give you the most control, give you the exact look you desire, and could be more effecient on the hardware.
I love the idea of unified lighting and the like, but even Doom 3 found "exceptions" where that approach did not give the best result. Giving artists control may be more time consuming in some ways, but it also ensures you get the exact result you want.
