Usually pricing is not determined by a classical calculation like cost + profit margin = consumer price.
It's the marketing department estimating what price they get away with. Internally Nintendo decided they can sell Luigi Mansion 2 HD for its standard price point and then let's not forget put some marketing behind it.
For Metroid Prime Remaster there was almost no marketing attached to it besides the Direct announcement. Just showed Nintendo did not expect a huge seller, which with 1 million +, it did do decent, but not mindblowing.