Yeah, the E2E input() method is sort of a nuisance as it does a find based on the ng-model of a particular input.. So for situations like ng-repeat, it doesn't lend itself to any practical use.
Good news is, you can get the functionality you want just using element().
element('my_element_here').val('Value I want to enter!')
expect(element('my_element_here').val()).toEqual("Value I want to enter!")
Basically, the element() call can be chained with any of these jQuery-esque methods:
val, text, html, height, innerHeight, outerHeight, width, innerWidth, outerWidth,
position, scrollLeft, scrollTop, offset.
The E2E Test harness for Angular is... interesting. And in desperate need of some TLC. But it's actually pretty good at what it does, once you get over the awkwardness of it! (And assuming you survive the documentation)