Well, new Aeon or not, I think he was right. Now, before the villagers storm the castle, I had better explain.
The decks Crowley would have been familiar with would have been the old Marseilles and Visconti decks, the Sola Busca, the early occult decks (Ettiella et al) and the GD decks. All of these follow an old, some would say outdated view not only of the occult, but of society in general. The "medieval" decks are representative of their times, as is the Sola Busca. The newer (de Gebelin, etc.) occult decks as well as the GD decks look back, at what has been done. They could be said to reflect a society that doesn't exist anymore, a feudal way of life that isn't relevant to modern sensibilities.
The Thoth, however, differentiates itself by looking forward. As a cohesive work, it introduces many ideas far more in tune with modern developments in science, spirituality as well as society than those older decks. It is a "corrected" deck. It puts women in a far more prominent role, it discards many sexual taboos, it suggests different sexual orientations, and goes further than other contemporary decks in acknowledging the winds of change prevalent in the 20th century, putting man at the center (not only of religion but of society as a whole, with the advent of increased awareness of human rights). Crowley knew that in order for a deck, or any other work of art, to be relevant, it would have to reflect changing attitudes.
Since he was in the business of occult science, he wouldn't have seen the use of outdated ideas, anymore than disproved scientific theories would be taught in schools for nostalgia's sake (creationism aside, of course). But I don't see anything wrong with that, especially if we're talking about subjective views. I mean, it seems like political-correctness taken to extremes, if the creator of a work isn't allowed to think his creation is the best, or be proud of it, but has to say his creation is no better or worse, just different. Should even the mere fact that he created a deck and liked it be held against him?