If you ditched one of the requirements and kept the other, you would still have a family pattern, but it would be easier for the names to be different. I think that with the initial and end sounds the same, the names will almost inevitably sound very similar. You could stick with your E and F pattern, or go with A endings?
Personally I think A endings is a wee bit nicer. Otherwise it sort of sounds like you are pairing off the kids IYSWIM. Twins particularly can resent being lumped together as they get older.
I think Isabella and Sophia are lovely, if you do go that route. There are loads of A names to choose from too:
Francesca
Clara
Sara
Adela
Natalia
Julia
Magdalena
Just to pick a few of different styles that spring to mind.
But like I said, if you don't mind the names being similar, just go for Emilia and Freya. You like them, and that's what counts. Think about shortenings too though. If you ever call Eliana Ellie, then an Emmy too would be really confusing!