Considering his father's history in Portugal and against the Braganzas (and Portugal's long standing ties to Britain), I have a hard time seeing the heir of Napoleon marrying the heiress of Portugal and making the Bonapartes the next dynasty in that country. I'm pretty sure the rest of Europe and even the Habsburgs would nix any marriage that would have Napoleon II be even the spouse of another reigning monarch. They wanted to keep him in Austria.
But he is not Napoleon II of Bonaparte, he is simply Franz, Duke of Reichstadt, from the House of Habsburg.
He is simply a consort, similar to Albert or Philip, Prince Consort of Britain, they have no physical power in running of their nation.
If Maria is happy to marry Napoleon's step-grandson, why not accept his son? At the end of the day, the boy did not really know his father, so as long as Astria keeps a close eye on him, I cant see him reaking revenge.
Also look at the relationship between Queen Victoria and Napoleon III, this could help, curb the Prussian army, with a France-Britain-Portugal-Austria alliance.