I have just finished writing up a long document that tries to give a comprehensive list of problems affecting academic research.
Writing this document is something that I had been meaning to do for a very long time, almost since I got started in academia in 2012 with my master's internship. Many academic practices did not make any sense to me already at the time, e.g., hiding research articles behind paywalls rather than simply hosting them online. I tried to ignore these concerns for a while, and did my PhD without questioning too much the order of things: for some practices I eventually saw a justification, but for many others I did not, and they made me more and more uneasy. So I thought that I should eventually come back to these problems, to re-examine my beliefs about the way academia works. Hence this long list of all the problems that annoy me, which I will try to keep up-to-date as time passes and my experience evolves.
Of course, complaining is always easy, so I have also tried to give some thought in the document about ways to fix these problems. The document does not mention my own initiatives in this direction (e.g., refusing to review for closed-access venues), which I will eventually write up separately.
So I encourage you to have a look at the document, What's wrong with academia?, and share with me any feedback that you may have!