I've seen less plausible stretches than than and can totally imagine
Minnie as a nickname for
Emmeline. I think
Minnie is a flexible enough nickname--kind of like
Mamie or Mimi--that I'd accept the barest of sound similarities as a reason to use it. :-)
I think
Emmeline and
Elisabeth would be great for sisters. They're both E names but I think they're long and different enough that it won't look like
Emmeline was picked just for the sake of having an E theme. And of all its possible nicknames, I'd much rather see
Minnie than something like
Emmy or
Emma.