The parallel with Promtheus was not unnoticed. The ending was great and the only part I have questions about is the fields of wheat on the surface.
1. At the end of Portal 1, we see a parking lot surrounded by a lush, green landscape, covered in trees. At the end of 2, we're in Ohioan wheat fields. Yes, it's a massive facility, but I didn't get the sense that we traveled very far horizontally, only vertically. Plus we wound up in GLaDoS' chamber again, so the elevator up should have brought us back to the same parking lot.
2. We're pretty much certain that the combine get a full defeat at then end of Episode 3, but this seems to promise us that the earth gets back to normal. Earth is lookin' pretty good now, with blue skies and abundant grain. This could also mean that North America is largely untouched by the Combine, as HL2 is in Europe somewhere.