What exactly do you find problematic about npm compared to the traditional package management systems (i.e. apt et al?)? I ask because having started using npm some months ago, I find it works better than anything I've ever previously encountered. Is there something I'm missing?
That's because you're using it as a developer. Trying maintaining software "packaged" using npm and shipping it to users later in a way that follows best practises. You'll want to kill yourself.