Aquemini is better, but ATLiens is SEVERELY underrated. It should've got 5 mics for production alone; it was a concept album, and the production reflected the same themes from the intro to the outro. And Aquemini doesn't really do that.
What Aquemini DID do, however, is present such a diverse selection of musical demonstration that it HAS to get nods over ATLiens. It's like a whole different animal of an album. It's like trying to compare a poetry collection to a graphic novel.