I have a data point:
My o3DS XL has the Samsung NAND chip (1,000,341,504 bytes), and I did a 7 wire hardmod for faster transfers. The TekRepublic TUC-300 card reader doesn't recognize it at all. The Anker AR200 USB3.0 works perfectly, and I'm getting consistent 20 MB/s reads and 14 MB/s writes...