Infanta Sofia has the same name than her grandmother Queen Sofia.
Queen Elizabeth has the same name than her mother "Queen Mum" Elizabeth.
So why should an aunt with a similar name matter?
Personally I really like Magdalena. It's been one of my girl favourite for years now and it would be really nice if Sweden would get a little Princess Magdalena. And to get a little hypotetical: What about twins? A little Princess Magdalena (to honour the aunt) and a little Princess Philippa (to honour the uncle)? Or even triplets with a little Princess Annemarie (to honour the aunt (Anna). And not forgetting the greataunt (Annemarie of Greece)) to the aformentioned two?
Ahhhhh, okaaaay ... I'm getting a little overboard here. But it's fun to speculate these things.