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It's always been said that they stayed with carts due to piracy but I suspect part of it was due to the fact that discs didn't allow visual upgrades as the generation went forward. With the SNES, Nintendo was able to use the FX chip to stay ahead, tech wise, of the Genesis. In the N64 era, they were also able to do this as well. Once the Gamecube was out, that option was off the table and has been ever since.

This is also why, imo, we're hearing that the NX will have "upgradable" tech. I think people mistook that as hardware upgrades and not something like what they did with the FX chip back in the day. Nintendo has always been keen on that sort of thing and now that they're going back to carts, the option is there again.