You probably could make a case for Barbarella or Danger: Diabolik as the work of auteurs and worthy of inclusion. Or perhaps the Lone Wolf and Cub films would sit alongside the numerous samurai films of the collection.
Maybe Altman's Popeye would qualify under the auteur standard. Same with Cronenberg's A History of Violence.
And, Oldboy.
Now, stretching it into new territory that is not necessarily marked by auteurism is another thing. A couple of thoughts.
Superman: The Motion Picture - obviously an important movie in the development of the genre.
Batman (1989) - might actually fit in better into the collection due to its expressionistic leanings and because Burton is something of an auteur, although I think Burton's auteurism is more defined in his other films.
Akira - Animation is not Criterion's forte, but I could see them expanding there and Japanese anime wouldn't be that big of a stretch.
Ghost World - It certainly would fit in with many of their indie movies. Plus Terry Zwigoff already has a film in the collection (Crumb).
American Splendor - Ditto it fitting in with their indies. Plus it would be a good companion to Crumb.
Now that I think about it, Fritz the Cat would be an interesting choice. The world's first X-rated animated feature would seem to count for something.