I agree with you in that simplicity is usually the way to go, at least that is what I try to accomplish: a truly intuitive and simple solution to organize my scientific literature. And for years now I have been doing research in a way similar to what you just described, having a collection of literature in devonthink, together with my own ideas in the form of notes and having the relations between all the literature in my mind when writing a paper. However, more recently, the amount of relevant literature I need to organize, understand their relations and keep everything in mind becomes too much to remember, since I am usually working on several projects at once. Additionally, I want something that I can go back to after a longer period of time and easily understand the relations between the papers without spending too much time. That is exactly why I want/need a visual way to organize the items in my database. I will do it for now with iThoughtsX but I am still hoping for a smoother way in the future.