Right now it appears that it's impossible to use angular2 directly from node_modules when typescript is targetting es6 because es6-shim.d.ts is indirectly referenced from zone.d.ts. This APPEARS to be a regression of #4882 that has happened because zone.d.ts directly references es6-shim.d.ts. This is confusing to me because zone.d.ts (in definitelytyped) has ALWAYS referenced es6-shim.d.ts and therefore this should never have worked.

The reference chain is:
core.d.ts -> ./manual_typings/globals-es6.d.ts -> ../typings/zone/zone.d.ts -> ../es6-shim/es6-shim.d.ts