In spite of what someone outside of a business mindset might think, a successful business does not set the pricing of their goods/services based on what the competition is doing, what the cost of delivering the goods/services are, how old the product is, how much use the customer will get out of the product, the quality of the product, etc., etc.
All of those types of things do factor in to determining the final cost to the consumer of the good/service - but, a successful (and "successful" is the key word) business ultimately sets their pricing based on one single thing... what the market will bear.
If Nintendo could sell NES game downloads for $50, they'd do it. But they know that won't fly today (though, I'd be remiss to point out that a few short years ago, people were gladly paying $20 for NES titles - some of which, I believe, put out some pretty impressive sales numbers... one of which was taking in some decent bank on eBay last time I checked - a quick look finds a completed auction for $12+2).
And while Nintendo would be wise to consider the age of the titles, what the competition is doing, the strengths of the games (Link's Awakening is worth more than the asking price, Tennis? eh....), ultimately, they're going to set the price at what the market will bear. If people stop buying due to the price, then they'll consider changing prices. However, w/r/t Wii downloads, I don't think the price is really what's hurting them. As for 3DS downloads, I don't really hear much complaining about 3DS eShop sales.