On shortcuts: you're just used to another way, it's not the system's fault. It's possible to use both Windows and OSX without much difficulty after getting used to it.
At least 50% of the joy of using a mac is due to the hardware and integration.
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.
The greatest shortcoming is the lack of packages. After using debian, homebrew is a toy.
1. Installing everything from source (normally I don't mind compiling, but large packages can take an hour or two. Ironically, OS X doesn't need to support many different architectures, so there's no excuse for not having binary compatibility like Linux does).
2. It doesn't manage the entire system. The process for installing from a .dmg or from the app store is completely different from homebrew, and the two don't talk to each other well (or really at all). I want a single source to manage all of my executable files and their configurations, not a small handful that each manage part of it.
In OSX, /usr/local is really user-space. It comes empty on an install, and the system never touches it (that means no mess with /opt). The FHS also doesn't mandate /usr/local/bin to be owned by root. Don't root-owned utilities go in /usr/sbin?