We did the next best thing after improving sydent: we wrote our own implementation of an Identity server: mxisd. We linked it several times in the doc. You should give it a look. That's one example of how you can be better at privacy.
If the content of the document does not surprise you, and you were fully aware of all that was going on, it is also a win! Sadly, this is not our experience with the many users we came in contact with. They did not know, but wanted to know in details.
We do not mention End-to-End encryption would be cool indeed because it would not change what is happening here. In Matrix, the encryption would only cover the content of the event, but not its metadata (sender, source, timestamp, etc.). The document is clear that the vast majority of the leaks are around metadata (who sent what, who did what, when, from where) and not data itself (the message itself).
This document only scratches the surface of privacy in Matrix, by being specific to Matrix.org and its choice of recommended software. It gets worse as we start investigating the protocol itself. It is your choice to see this as FUD. It does not make it less true, and while you might not care, some do. We published the document for those who care and do not have the means, time or capacity to do such a research themselves.