Nintendo follows a Disney-like model. Rather than trying to sell as many copies of a game as they can in its first run by cutting prices, they'd rather sell as many copies as they could at full price and then bring it back in some fashion a few years later. Disney has had a habit of introducing enhanced versions of movies that have few differences, Nintendo does that or adds a new entry to a series that releases once per console. By not cutting the price they are reinforcing the idea of a lasting value in their products, at a level that includes the whole range. If they had cut MP Trilogy's price rather than its production the message would have continued to be "just wait, you can get it cheaper eventually." Instead, they could rerelease it on the 3DS in two years if they want and charge full price again because people would realize that no matter what a full-priced 3DS game costs that is the best price they're getting it for.
On the flipside, games that rapidly decrease in price aren't worth full retail. Why would anyone buy Ninja Gaiden 3 at $60 when they know that in a few months it'll be $40 like NG2 was? Also, if you know the company is willing to sell the game at $40, which means they still make a sale per unit, then it makes THAT company seem greedy for trying to sell a product at $60 that isn't really worth that price to most consumers (or even in their own business model). Early buyers of a game that gets cut in price quickly are basically being suckered in. They want the game so they pay extra to have it, but the company is happy to take far less - that sounds a lot more greedy to me than what Nintendo does (even though I know it's reasonably not).
Overall, it's a method to protect the value of Nintendo's franchises. Even a small-time game like Excite Trucks could have hurt the sales of SMG if people expected the same old price-cut-on-lagging-sales model. Nintendo may not have maximized its profits on some games because of this, games they probably won't even consider for rerelease, yet it helped to maximize profits on the big games (and thus overall). Also, they aren't hurt if Excite Trucks doesn't sell an extra 250k at a reduced price, as they stood little to gain from those sales and a lot to gain from the fact that people would have to buy the big games at full price if they ever wanted it new at all.
tldr - Nintendo is trying to protect their brand name and long-term viability while most of their competitors don't believe they have either, and really don't unless they can produce far more content than Nintendo does.
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