1) The lack of packages combined with lack of quality of the packages (e.g. they do not build or have a poor defaults).
2) That homebrew installs stuff under /usr/local as owned by your user. That does not meet the expectations of UNIX applications and seems to me like it could be unsafe due to messing with expectations. Stuff under /usr/local/bin is supposed to be owned by root:root.
The good part of homebrew is that writing homebrew scripts seems easier than writing dpkg or rpm scripts.