I remember somewhere I did a quick and dirty analysis on the difference using store bought BR-RW vs SD Flashcards and the difference is less then $1US. And considering that Nintendo usually recommends a certain size to help bring the cost down by buying in bulk. My guess is they will either go with the 64GB or the 128GB sizes for games with maybe a little extra for i/o.
The two downside to carts of old was the battery back up which isn't used anymore since they can write to the flash memory now, and the cost which ever since smart phones, digital camera, etc became a consumer item, the price of manufacturing flash has plummeted.
So it is a pretty solid move by Nintendo for this.