I've also spent a lot of time thinking about this problem and would like to eventually put some work towards it. A couple of additional ideas that I've had:

* A paper could rely on a critical reference to build upon and the referenced paper could be disproven down the line but this is not immediately obvious from the paper that used it.

* Currently it doesn't seem like any merit is given to researchers who are very good at reviewing papers. Compare this to software where a good code review is celebrated. Editing and cleaning up the state of science should be valued when scientists are looking for work so I think that something along the line of a Github CV for scientists would be valuable.