Two kids with the same initials could easily be a coincidence rather than a determined theme. I'll bet most folks don't even notice it, and I don't see switching things up as problematic at all. Of your lists, I best like
Susannah Mae,
Emelia Madeline,
Benjamin or
Simon to join
Elisabeth and
Ethan. For honoring purposes, I'd be willing to go with an "M" middle name for
Benjamin or
Simon but I'd really prefer another beginning sound. For me,
Thomas Matthew and
Jacob Mitchell sound best. I love
Elliott, but if you are wanting to avoid an "E" theme, how about
Matthew Elliott?