Kotofej, the bundle system works well...once you get it setup correctly.
This.
I'm a big fan of the Autoloader mechanism, actually - I use it both for my own daily work for custom internal tools, as well as SincPac.
I also publish a few of my smaller apps at Autodesk Exchange, and merely pointed out Autodesk's historical pattern of introducing something, and being okay with things not being what they could be; this is no different than many of the long-standing bugs, etc within AutoCAD itself.
Another example of this, with regard to Autoloader, is custom system variables - Int variable type is not properly implemented, the way string types are, and there is no means by which to implement a bit-coded sysvar via PackageContents.xml directly.
I didn't mean to deter you from Autoloader, as it is exceptionally good at the few things that it does; as Jeff aptly points out, you just need to be mindful to use it well.
Cheers