I'm don't even sure the portrait on geneall.net is really her. As you say, MA is said to habe been unattractive and this girl is cute, and I think this dress and hairstyle are not very compatible with 1790 or even later (because this girl seems to be a least 11 y.o. and if it's Maria-Amalie that would make 1790...)
The dress looks like 1790's style to me, but I could be wrong. Perhaps CountessKate knows if the dress and hairstyle are from the 1790's.
I would have to say that the dress and hair in the portrait looks rather more like one from the 1760s or at the latest, the early 1770s - the stiff pointed bodice, the high hair are similar to portraits of this period rather than to the 1790s. If one looks at a portrait of Maria Amalia's exact contemporary, Maria Christina of Bourbon Two-Sicilies, the style is very different. This is the latter, portrayed in 1790 by Vigee Le Brun:
That's exactly what I wanted to say when I wrote that Maria-Amelia's little picture wasn't really compatible with the fashion of the 1790's, for young girls.
I was precisely thinking to this portrait of Maria-Christina of Sicilies by Mme Vigée-Lebrun, and also to another exact contemporary, Madame Royale (Marie-Thérèse of France, Louis XVI's daughter) painted by Mme Vigée-Lebrun, by Wertmuller and by Dumont between 1785 and 1789. Everywhere we can see this same type of dress (more or less a "gaulle", the trend started by Marie-Antoinette), no corset but a high mousseline waistband, and of course the hair without powder and arranged in low soft curls...
So, I have strong doubts about the little picture of geneall.net... by the way I've noticed that there are sometimes some mistakes in the identifications of this site - like everywhere else, it's true.
I think that the girl next to Infante Antonio in Goya's family portrait is Maria Amalia. Although she was dead, she was painted with the rest of the family as a way of stating that they still remembered her. Besides, it was common to have portraits of deceased royals made for their family. For instance, there were at least 3 portraits of her grandmother, Louise Elisabeth of France, which were painted after her death. Why? Because her family wanted to have portraits of their beloved late relative.
That's true. For example, in the famous "Louis XIV's family" by Jean Nocret, we can see Anne of Austria and Henrietta-Maria of France, and several children, who all were already dead when the picture was made. There is also many portraits of Louise-Elisabeth and her sister Henriette of France, who are also postumous, and so on...
I think that Maria-Amelia is indeed the woman on Goya's painting.
First because she's very close to Antonio, really like a husband and his wife.
And secondly because if it was Carlotta-Joaquina, why her husband wouldn't be there too? Maria-Louisa is in the picture with her husband Louis of Parma, so Carlotta-Joaquina should be with her husband the future Joao VI...