ES2015/commonjs interop currently sucks with TS. This is how you only import flatten:

  import flatten = require('lodash/flatten')

TS expects any modules imported using ES2015 import to have the shape of a ES2015 module. This is an issue for many UMD/commonjs modules. In the case of lodash, it's effectively doing this:

  module.exports = flatten

And then you're importing it like so:

  import flatten from 'lodash/flatten'

and that is being transpiled to something like:

  var flatten = require('lodash/flatten').default

Note the default.

I haven't migrated to webpack 2, but some brief experiments suggest all modules get massaged in to ES2015 format.