Although Meteor does not recompile packages installed in node_modules by default, compilation of specific npm packages (for example, to support older browsers that the package author neglected) can now be enabled in one of two ways:
Clone the package repository anywhere in your application outside of node_modules, make any modifications necessary, and then use npm install to link the-package into node_modules:
npm install imports/the-package
Meteor will compile the contents of the package exposed via imports/the-package, and this compiled code will be used when you import the-package in any of the usual ways:
This reuse of compiled code is the critical new feature that was added in Meteor 1.6.2.
Install the package normally with npm install the-package, then create a symbolic link to the installed package elsewhere in your application, outside of node_modules:
npm install the-package
ln -s ../node_modules/the-package .
Again, Meteor will compile the contents of the package because they are exposed outside of node_modules, and the compiled code will be used whenever the-package is imported from node_modules.
Note: this technique also works if you create symbolic links to individual files, rather than linking the entire package directory.
In both cases, Meteor will compile the exposed code as if it was part of your application, using whatever compiler plugins you have installed. You can influence this compilation using .babelrc files or any other techniques you would normally use to configure compilation of application code.