This is a cultural problem, not a module management problem per se. Blame the author of module C, not the package management system.
Semantic versioning's raison d^etre is to prevent these sorts of issues. Reusing a major version number is supposed to constitute a promise not to remove or change the call signatures of any functions published by your library. This is necessary so that a dependent library can declare a dependency on version 1.x.x of your library when version 1.1.0 is released, without having to worry that version 1.2.0 of your library will break things.
The problem is that too many library and module authors (who are otherwise talented, or are simply the first provider of a useful library that ends up gaining traction) refuse to follow the rules, and there's no effective sanction in the OSS marketplace for this sort of antisocial behavior.
As soon as backward-incompatible change is introduced without bumping the major version number, the dependent module author becomes paranoid (and being closer to the user, he's going to wrongly get a disproportionate amount of blame), and (rightly) feels he has no other option but to declare a strict version dependency. And when there is more than one dependent module involved, the misbehavior of the independent module author can cause a dependency graph that is impossible to satisfy.
As far as I can tell, this whole situation started with Ruby, and is the main reason (along with second-class documentation) why I am generally averse to its ecosystem. rvm and its ilk shouldn't even have to exist.
> Semantic versioning's raison d'être is to prevent these sorts of issues.
Semver may surface them by making it very clear (assuming all involved libraries use semver) where they can occur, but, if you have a package management/loading system that only allows one version of a particular package to be loaded, obviously can't do anything to prevent the situation where different dependencies rely on incompatible versions of the same underlying library.
Sure, with semver it won't happen if A depends on C v.1.0.1 and B depends on C v.1.4.3 (as A and B can both use C v.1.4.3), but it will still happen if A depends on C v.1.0.1 and B depends on C v.2.0.0.)
To actually avoid the problem, you need to isolate dependencies so that they aren't included globally but only into the package, namespace, source file, or other scope where they are required.
That's all good and well, but these packaging problems happen and they'll continue to happen, so wouldn't you rather have a system like npm that can tolerate mediocre packaging than one that doesn't? When you're trying to fix clashing dependencies, are you really going to care about whether those clashes are an intrinsic or a cultural problem?
Regarding semantic version: it works in theory, but in practice applications often ends up relying on bugs, private APIs, or other kinds of non-public behavior. For example the GNOME libraries have been following semantic versioning forever, yet sometimes an upgrade breaks something else because that something else was relying on a bug. In 2004 there was a famous case where upgrading your glib would break gnome-panel. This is of course not to say that semantic versioning is useless, but in practice you will still need some kind of version pinning system.
As for "rvm and its ilk shouldn't even have to exist": you do realize that rvm and its ilk are not just to allow you to pin your software to a specific Ruby version, right? They're also there to allow you to easily upgrade to newer versions. Let's face it, compiling stuff by hand sucks, and your hair has turned white by the time the distro has caught up.
Semantic versioning's raison d^etre is to prevent these sorts of issues. Reusing a major version number is supposed to constitute a promise not to remove or change the call signatures of any functions published by your library. This is necessary so that a dependent library can declare a dependency on version 1.x.x of your library when version 1.1.0 is released, without having to worry that version 1.2.0 of your library will break things.
The problem is that too many library and module authors (who are otherwise talented, or are simply the first provider of a useful library that ends up gaining traction) refuse to follow the rules, and there's no effective sanction in the OSS marketplace for this sort of antisocial behavior.
As soon as backward-incompatible change is introduced without bumping the major version number, the dependent module author becomes paranoid (and being closer to the user, he's going to wrongly get a disproportionate amount of blame), and (rightly) feels he has no other option but to declare a strict version dependency. And when there is more than one dependent module involved, the misbehavior of the independent module author can cause a dependency graph that is impossible to satisfy.
As far as I can tell, this whole situation started with Ruby, and is the main reason (along with second-class documentation) why I am generally averse to its ecosystem. rvm and its ilk shouldn't even have to exist.