I am a Charlotte, born when it was more popular than it is today. I was lucky as I was the only one in my year throughout primary school but I did end up meeting quite a few others later in life. Fortunately, there's so many nicknames associated with Charlotte that it wasn't really a problem - Charlie and Lottie being the obvious ones. At university I was known as 'little Charlotte' (!) for a while until friends started distinguishing me from 'big Charlotte' by my surname (which, luckily for me, is also a given name). I can't recall ever being annoyed by it and was always pleased to have a classic name. However, if you've got a really unusual name yourself, you may feel quite strongly against picking something in the top 25.
Josephine is one of my own personal favourites - I must like 9 letter long feminisations! I think it is pretty and due for a comeback. It lends itself to lovely nicknames like Jo, Josie, Posey, Fifi, and so on.
I think the great thing with a longer name is that if your daughter is in class with another with the same name, you have the option: she could be Charlotte X or Lottie or Charlie; Josephine Y or Josie or Jo or Posey or Fifi.
If you like Charlotte and Josephine, you might also like Alexandra, Caroline, Clara, Clementine, Cordelia, Frances, Georgia, Georgina, Helena, Juliet, Louisa, Margaret, Matilda, Millicent, Rosalind, Theodora, Susannah and Winifred.