Reason why I mentioned Digital Distribution in the first place is because, like some have said, it would probably be cheaper. Thats why some titles like Mega Man 9 and 10 could be so successful, because they had a small budget and released the games digitally, which saved a bit of money. The same could be done for AAI, but DSiware may be too limiting.
If I were to get a straight 3DS port, I'd expect some extra bells and whistles (costing money to do) to justify a $40 pricetag, but with a 3DSware-like title (I say that becaise 3DSware hasn't officially been announced), I wouldn't mind the title lacking things like 3D for example..though a 3D AAI would be cool...*imagines using Little Theif in 3D*...