I've been waffling over this very question lately.
I give the edge to Patek on this one. That says less about the AP, and more about the high regard that I have for the 3940. In my opinion, it is the platonic ideal of a perpetual calendar. I do not believe that a more successful perpetual calendar came before or after it.
However, the 25668 should garner more respect. Only 205 were produced across all metals, AP could only produce a small number per year because of the amount of work, and the AP perpetual calendar movement is special. The gold on gold has character in spades, and it is just such a special watch to look at. I am a real sucker for the font that AP used for the logo.
The only negative, in my opinion, is that the case is not as lovely as the 3940. I feel like the 3940's case is absolutely timeline. The AP feels like a watch from the 80s or 90s - whether that is good or bad that is up to you!
Between the two, you cannot go wrong.