I think Alex and Daniel work fine with Charlie and Sam. Nathaniel does seem a little long compared to the others but the style is basically the same. Would you consider Nathan or Nate?
Charlie, Sam & Hank (Hank can be a nn for Henry or stand on it's own)
Charlie, Sam & Toby (Love this! but i'm not really fond of the longer forms - Tobias, Tobiah or Tobin.)
Charlie, Sam & Abe (or Abram)
Charlie, Sam & Leo (It can be short for Leonardo, Leonard, or Leopold but it's definitely used on it's own.)
Charlie, Sam & Luke (A lot of people named Lucas, Lucius, Lucian end up using Luke anyway - I know a few.)
Charlie, Sam & Reed (Not a nn but short and sweet like the other two.)
Charlie, Sam & Liam (Some use it as a nn for William but I've seen people use just Liam as a FN.)
All of the girls names work very well with Charlie and Sam. My favorites are Isla, Iris, and Harriet nn Hattie. I think it's fine to give a girl a longer FN.
How about Nate? Nathaniel is too formal with a Sam & Charlie, but Nate is Great!
I like Charlie, Sam & Leo. They sound great together!
Or, how about Charlie, Sam & Theo?
For a girl, I like Charlie, Sam & Maggie or Charlie, Sam & Kate :)
I find it funny when parents try too hard to match sibling names. They are all individuals who will have their own lives.
I think Charlie, Sam, and Nathaniel sound fine together. Nathaniel is a great name.
from your girl names I like Iris and Elisabeth
I would say stick with short names. However, I don't think opposite gender sibs need to match. Elisabeth and any other longer, more formal girl name is fine.
For boys, I'd go with names like