Nietzsche's thought is brilliant, but most people don't think of how screwy its repercussions can be. First of all, if the eternal recurrence means we repeat every atom and combination of atoms in every possible way, this means that we don't merely repeat the exact lives we're living right now, but an infinite number of modes of our current lives as we understand them. I'm not just the recurred John the shrink with a love for good books, writing, and guitar, but also the recurred John the child psychologist with a love for good books, writing, and guitar; and then John the child psychologist with a love for mediocre books, writing, piano; etc. The point is that the claimed value of the eternal recurrence -- that we will repeat our lives endlessly, and so much develop a sense of embracing these possibilities -- negates itself because we're not just repeating the lives we know right now, but also an infinite number of possible modes whose identities could be related to our identity now.
Second, even if it were exclusively the case that we repeated this life and this life only, saying we should embrace this possibility -- amor fati, as Nietzsche would say, "love your fate" -- doesn't really mean anything, given that when we do recur ourselves for a second, third, infinite number of times, we're always doing so with a blank slate, ignorant of our previous (or future) lives. The claim that we should embrace these future lives because they recur doesn't mean anything, given that saying they will recur has no relevance to our consciousness, given that with each recurring we will have no knowledge of our past recurrings -- and if we did, our life technically wouldn't be recurring, given that this knowledge of a past recurring would have resulted in a different way of looking at and interacting with our world. Bill Murray's character in Groundhog Day isn't a fair comparison given that he knows of his recurring days.
Moreover, Nietzsche's claims verge into physics. If you're down with a big crunch view, presumably you'd be a good fit for an endless universe. But if you think the universe had a beginning, even if it was 14-16 billion years ago, you're significantly limiting the possibility of an eternal recurrence of all things. Briefly, an eternal recurrence presupposes an eternal universe.
Miguel de Unamuno was on to something when he said that the eternal recurrence was Nietzsche's way of gaining eternal life. It all comes back to psychology, it seems.