Maybe it's because I'm not the biggest Unix purist, but I don't really mind the proliferation of command line options. The two things that do irk me are:
* Using short options in scripts. Scripts should almost always use long options. As a corollary, tools should always provide long options unless the tool isn't intended for scripting.
* Lack of discoverability. We still don't have a standard way to ask an arbitrary tool which flags it supports, or for a rough semantic mapping of those flags (e.g. the classic -v/-V verbose and version confusion). Developing a standard here would go a long way towards automating things like tab completion without each tool needing to maintain N scripts for N shells or having its own slightly-different `--completions=SHELL` generator.
* Using short options in scripts. Scripts should almost always use long options. As a corollary, tools should always provide long options unless the tool isn't intended for scripting.
* Lack of discoverability. We still don't have a standard way to ask an arbitrary tool which flags it supports, or for a rough semantic mapping of those flags (e.g. the classic -v/-V verbose and version confusion). Developing a standard here would go a long way towards automating things like tab completion without each tool needing to maintain N scripts for N shells or having its own slightly-different `--completions=SHELL` generator.