I think Ellie can, and does, stand on its own just fine, although I prefer it as a nickname. It could be mistaken for Allie occasionally, but I don't think that should be a dealbreaker. The same could be said for any two names that rhyme.
Between the two, I prefer Allie (but, remember, I am an Alison, so...). I think Ellie is okay, though, just not for me. Even if I used a name like Elizabeth or Elinor, Ellie wouldn't be the nickname I'd pick for it.