There are sooo many different apps that can create a great system.
But the problem with all of these programs is that they were designed by someone else, not you. Even when an app touts itself as "flexible", there are still limitations both code-wise and design-wise. There is no perfect app.
But there's one tool that could be used exactly how you want it to be: paper.
Paper has no limitations whatsoever. You can just create whatever you like, however you like. And that's why it's ...
Gosh, I feel like I've written about this before...
I just re-watched (for the 10th time) this talk. It is about evolving education in the right way. In it, Ken Robinson talks about creating the right climate for change.
Think about it... Instead of trying to force people to change, try creating the right climate/atmosphere for change to occur. Natural change means change to the fullest. In the best way possible.