I have only little experience with unity3d, I prefer 3dgs, especially after I upgraded to commercial, a new world opened up.
unity is definitely a well developed engine having a lot of advanced features (mainly available only in Pro which is very expensive), and more up-to-date in technology, has a nice editor, but requires some 3d knowledge to start with, and a bit more organized work and pre-designed game concept because of object oriented programming. its editor has a lot of features what makes life easier, and what I would like to see in the new WED, like terrain editor, vegetation editor, particle editor, and how game objects can be built up from components, and everything can be seen in real-time.
personally I like the simplicity of 3dgs usage in contrary with unity omplexity, but in 3dgs there are a lot of things you have to do by yourself if you really want to utilize all the engine features effectively - this is why I made my own game editor instead of using WED.