I honestly have no idea what you're talking about.
The reason DirectX is installed on your system as opposed to being packaged with each game is so it's system-wide, so you don't have fifty versions of it scattered about your hard drive.
In other words, it has an installer to prevent the exact issue you're talking about.
When an API (or library in general) is packaged with the piece of software using it, the problem is that it becomes very difficult to update it. After all, if you have twelve programs using Direct3D, and every single one of them has its own local copy in its own directories, how do you update Direct3D? Each piece of software would have to handle it on its own. However, it's installed in a system-wide manner exactly to prevent this.
This ties in to your other (almost as false) point: DirectX does NOT keep countless versions of itself lying around. Versions up until 9 were backwards-compatible with software intended for prior versions; versions starting with 10 are not, but include the legacy API for compatibility purposes.
EDIT: Wait, are you running the installer for every single game that says you have to install DirectX? You realize you don't have to do that, right? If you got install Diablo II and it bitches at you to INSTALL DIRECTX 4.0 OR DIE, you don't actually have to, because you already have that or better.