Cydia is a front-end for Debian APT, a mature packaging solution for Unix systems, designed to be a fully-featured replacement for Installer.
Why: BSD Subsystem has many bugs in it. You can't even change your password anymore. These issues are easy to fix, but no one in charge cares to maintain it. Most platforms have well-maintained userlands with fine-grained, dependency oriented package management. Telesphoreo aims to provide that. Cydia is your gateway.
Note: BSD Subsystem (obviously) conflicts with this package. Its files will be uninstalled, replaced, and generally upgraded during the installation process. As you can't "uninstall" it from Installer, it is important that you don't upgrade it when new releases come out. If you haven't installed it yet, you also should not. Instead upgrade to or install "Fake" BSD Subsystem, a package which is safe but otherwise pretends to be BSD Subsystem.
For help with either Cydia or iPhone/Java, please join the IRC channel #iphone on irc.saurik.com.