My main problem with discs is that you can't do anything with them. The format is fixed on ship.
With cartridges or cards, you only have to match pins, and you can do anything after that on your side. So it allows stuff like IR carts, or Boktai's light sensor, etc.
Of course, this also requires you to design pins that can generically send/receive data. If they're all dedicated to data throughput then you're screwed.
The upside to discs is you can print multiples and they don't cost much more or take up that much extra shipping space in the box.