1. Mixing up certifications (degrees that people get to help getting a job) and research / education. One might even split research and education. But certification/signaling is the big problem for me.
2. There is no market nor collaboration system for small ideas, or partial ideas.
As an academic, you either publish a paper or not. So small but very good ideas of good value do not have a good vehicle. Both to get accumulated, found by others and recombined. And to get credit / value from (incentive)
3. No incentive and no funding for infrastructure / quality / connections of data.
The lack of linking between papers to their refutations is partly because nobody has done it, because no institution invests in infrastructure.
This complaint is also that showing that a paper is flawed isn't getting rewarded, or not even getting published!. (@jamesheathers
and @sTeamTraen have elaborated on this a few times)
Skeptics finding faults in the literature should be richly rewarded.
But no one pays for those things for whatever reason....
PS. Thought triggered by this MarginalRevolution post