Thanks Anonymous. All true and correct. As I've been piecing this together, I've put the info in the various profiles, but it's not all in one place.
In his will, Samuel called for James and Margret to care for his children, and made William his executor (will is linked in his profile, and the image is clear and the handwriting legible). As far as I can tell, the McMillen family lived in Buffalo, Washington, Pennsylvania from before Samuel was born until three of Samuel's children and their uncle James moved to Iowa around 1872. Samuel's daughter (Maggie and Lizzie's sister) Nancy stayed in Pennsylvania with Samuel's siblings William and Margret until they died, then she moved to Iowa about 1902.
The 1870/1880 housemates don't match up exactly, but I don't think that's much of a problem. In 1870, Samuel's children Maggie (shown as the younger Margaret), Nancy, and John lived with the three older McMillens and Ella in Buffalo. I don't know where Lizzie was at that time. By the 1880 Census, uncle James had died, brother John was married (in Iowa), Nancy had stayed in Pennsylvania with William and Margaret, and Maggie, Lizzie, and Ella lived together in Indianola.
One of the family oddities is that some of them (Lizzie and John, for example) reported being born in Ohio rather than Pennsylvania, and some of them, like Ella, switch back and forth. Buffalo Township is close to the Pennsylvania/Ohio line, for what it's worth. I haven't found any Ohio state documentation for any of them.
I've made contact with a McMillen descendant who has posted some great info on FaG. She doesn't know who Ella was, either. Ella can't be the daughter of Samuel or his brothers John or David (they died too early). James and William never married as far as anyone knows. William's will left everything first to his sister Margaret, then to his nieces and nephew. I'm told James also left a will in Iowa, but I haven't looked it up yet. If Ella was the daughter of one of Samuel's sisters, her last name McMillen needs some explaining. Timing-wise, she could have been the daughter of any of Samuel's children, but again that would need some explaining. I am beginning to suspect Ella was born out of wedlock.
There also seemed to be a lot of dying young in the family. Samuel's daughter Mary Ellen died of TB in 1870, which probably explains that. Maybe that also explains why Ella disappeared after the 1880 Census?
Edit to add - James McMillen died intestate in Warren County, Iowa in 1877. Probate docs are on Ancestry. His only heirs were his siblings William and Margaret, and his nieces and nephew Margaret, Nancy, Elizabeth, and John McMillen. No mention of Ella.