I have always thought that systems should be something integrated. Each “system” has its own conventions, cultural values, etc. and I think you have to respect that. I believe in the Debian way (adapting programs to an integrated system, not just creating a large collection of packages that are identical to the upstream versions), I like to adapt my style of programming to the language (indentation conventions, identifiers, tools for building and testing, etc.), I prefer cross-platform applications that look and feel like each platform they run on, etc.
In the same way, I feel that the mere idea of having a programming-language-dependent packaging system is a broken idea. I know it has advantages, and I know that being specific to the language, some things work better or are more flexible, but I just don’t believe in that idea. Why should I use a different packaging system for certain things just because they’re written in Ruby? Why do I, as a user of those programs/modules, even have to know that there’s some Ruby-specific packaging system, that doesn’t integrate at all with my system’s packaging system, and mixing both leads to a mess?
Not only that, but Rubygems in particular is quite hostile to repackaging into a platform-specific packaging system. A lot of people only provide the gems for their software, which are harder to work with than “normal” tarballs. They also use their own conventions for directories, that break the FHS (for example) and basically only make sense in the context of Rubygems. In that sense, CPAN is much better (although I think using it for application deployment is a very bad idea, but that’s a different matter), because at least it installs everything in sane directories, it doesn’t change Perl in any way, and it’s not a special format, just a repository of easy-to-install, easy-to-work-with, easy-to-hack, easy-to-repackage “distributions”.
Why, oh, why?