Wow, I'm glad someone brought this up because I actually know exactly why Nintendo does this. It's really quite simple, but I'll go ahead and explain this so all baes are covered and no one can argue.
The story starts when Satoru Iwata is a kid. See, he's from Japan. If you aren't aware, Japan is home to the world's oddest things. When he was a kid, he had a bootleg laser light shined in his eyes. At first, his eyes just had a slight pain, but thought it would go away because it was just a light. But things got worse. And worse.
He ended up seeing an eye doctor about this problem. The doctor told him the most shocking thing he would ever hear in his life. This laser light actually left a hole in each of his lens' in his eyes! He could barely see, but he had no options at all for this problem. He was prescribed some glasses, which allowed him to see, but his vision was very blurry. He still wears the same kind of glasses, but that's not important.
Let's move forward for a bit. Satoru Iwata starts to lose some of his vision, even with the glasses. He is told that he needs laser eye surgery, but he couldn't afford it. He didn't know what to do. The glasses were good enough until he could afford the surgery, but he couldn't live off just the glasses all of his life and he knows this.
When Satoru Iwata could afford the laser eye surgery, he gets it right away. He could see clearly now. But, there was one problem because he waited so long to get his eyes fixed. He became colorblind.
Nintendo loves Satoru Iwata, so as a tribute to his greatness, they only use two colors on the discs. Satoru Iwata has been quoted to say "I am flattered." Nintendo thought it would be the best way to repay Iwata.
So don't complain. Think about it. If you're complaining about the discs only having two colors, you're not just dissing Nintendo. You're making fun of a colorblind genius. Satoru Iwata.
