I really don’t think it is fair to blame it on Java. Having very little native dependency is a huge plus to an ecosystem (just look at what Java will be able to do with Loom thanks to the almost all-Java dependencies). Also, Java was particularly keen on downloading class files at runtime, so linking everything was not even possible.

And it is not even a difficult thing to fix without going the linker way: java’s modules essentially solve it (as well as javascript modules could/can) — just specify what is visible outside a package and both ecosystems can “tree-shake” non-used code (though I dislike this nonstandard term)