Arunoda – his github name – recently wrote on Medium about a similar concept being applied (hopefully) soon in Meteor, whereby npm could serve the same function as Meteor’s Atmosphere.
The idea is that it simply takes a Meteor “wrapper” function to tell Meteor it’s an actual Meteor package (which is really just basically a require() and respect of folder/file structure – not literally but that’s the basic concept) and integrate with your Meteor app.
It’s simple enough to repackage any npm module for Meteor, so why not make Meteor do the heavy lifting by simply passing an argument at install like- meteor/app$ npm install -meteor lodash.
I think your idea has merit but it would be best if we could all agree on a single package manager, first.
Things that are relatively universal, like a language translation pack would be far more useful that way.
Edit – forgot I was typing on Medium and not Github :)