Just in case it helps:
Emilia origins = ancient Roman family name, used by Shakespeare; closely linked to Emil (boy) and Emily (girl) . Emily is the English version of Emilia.
Amelia is the English version of Amalia. The origins of Amalia = from the German word for work. Amalia/Amelia was popularised in UK by the Hanoverian kings of Britain. Amelie is the French version of Amelia.
The following may not matter to you in the slightest. It's not meant to be a criticism. If you like a name, then use it! However, as others have said, both Emilia and Amelia and variants of them are very popular at the moment, and the popularity of all these names has been rising (except Ameila, which is no 1 and can't rise any higher).
Amelia is the most popular, Emilia is the least popular.
Amelia = no 1 in England and Wales, with over 7000 babies named in 2012 (these are the latest figures)
Emily = no 4, with over 4000 babies named
Millie = no 26 almost 2000 babies
Amelie = no 51 over 1000 babies
Emilia = no 56 over 1000 babies
Altogether, that's over 15,000 babies named Amelia/Emily and variants in 2012.