Atiba, when I saw the title it immediately got my attention, as I have the same feelings toward this kind of tools. I use them — I’m a maniac of them — but at the same time they tend to distract me from both from the vision and from the practical actions.
Also at work, where I think these tools are quite necessary, they tend to have drawbacks similar to what you described.
I’m a software developer, so I couldn’t help but to design my own tool to have a more clear vision, but I’ve used a lot Evernote too (and still do). As you know, a mix of notebooks and tags can do miracles.