Is the reason you don't like Emma the popularity? Because if so, I'd suggest Gemma, which is less popular, but similar to Emma. Otherwise, I don't think Amelia and Emmeline are that similar that you absolutely can't use them, especially if their nicknames are Millie and Emme.
Another suggestion would be to use Caroline. Amelia and Caroline would be a nice sibset.
Yes, the only reason I'm not as fond of it is the popularity. Emmeline didn't even rank in the top 1000 names. I'd probably mostly be calling them "Millie and Emmeline".
I do love Caroline, and would have used it, but a family member already did (it's a family name), so this was a kind of compromise for me. :)
They are terribly similar, and I think you might run into pronunciation problems with Emmeline, as well. I've only ever heard it pronounced Emma-leen. Purely food for thought, but, as a younger sister, I would not have enjoyed having a version of my older sister's name. I love all the other names you listed, especially Rosalie and Marianne.
They are actually pretty similar. Amelia is almost like Emily, and Emmeline comes from Emily. And really, Millie and Emmy are even more similar.
Adaline -Addie & Millie
Abiline - Abbie & Millie
Coraline - Cora/Cori & Millie
Names I think go well with Amelia:
Abigail - Abbie & Millie
Juliet - Julie & Millie
Corinne - Cora/Cori & Millie
Winnifred - Winnie & Millie
Charlotte - Charlie/Lottie & Millie
Cecilia - Ceci & Millie
Lucille - Lucy & Millie
Wilhelmine - Willa/Minnie/Mina & Millie
Elinor, Rosalie, Margaret, and Marianne all go well with Amelia, as they have that vintage and elegant feel to them. I recommend spelling Elinor as Eleanor, as its the spelling everyone will think it is anyway. Ellie & Millie, Rosie & Millie, Margo/Maggie/Peggy & Millie, Mary/Annie/Rina & Millie
As you can see in my signature my daughter is Emmeline Amelia Story. I got told Emmeline and Amelia were far to close to put next to each other, some told me they were unbearably close. Clearly, I didn't let them stop me!
I have had nothing but praise for Emmeline's name, so I think you'd get double the praise for two named Amelia and Emmeline.
I love both names!
P.S. Oh but only one issue I would have, my daughter goes by Milly... So people may call Emmeline, Milly and then you could have serious issues! But it's not that big of an issue!