Read the WN. Rem is without doubt the "main character" of arc 3, but Emilia certainly took back the main heroine spot on arc 4 and 5. Her character got more developed later on. Well, I still love both of them, though.
And about alternate ending; there is actually one where Subaru eloped with Rem on that one scene. Again, just check out the WN - the author actually wrote one. It's very heartwarming, and Rem certainly attained her well-deserved happiness.