Nintendo did a very logical, yet un-business like thing. By doing it like they did, they have maximised total utility not only for themselves, but their customers too. While it is true they could have gone for much greater short term utility for themselves and mealy drop the price without warning or compensation, which would have been something very quarterly business like, but it isn't an American business.
Remember, while those free games are effectively lost sales from an accounting point of view, per unit they cost next to nothing and it brought Nintendo something money can rarely buy, goodwill(For most) and word of mouth frenzy. Now, if say EA was running the show, Nintendo would have simply dropped in a bundle and called it a day till the next quarter. Nintendo normally runs a much longer game than this and were punished this year for playing the quarterly profit chase with the botched launch of the 3DS. Nintendo has the benefit of a much more understanding stock holder culture which look for more real gains than pure gambling that is Wall street.
Yes, there would be a bunch of "Gap" people who play the system that maximise their own gain, but this is one of those rare situations Nintendo chose, where everybody wins. Including me.
I brought a 3DS second hand for $300NZD, which works out to $250USD(Changes a lot daily), which is still over-priced compared to other territories(480NZD), But I would have happily paid $300NZD price had Nintendo released it fairly at this price. As I see it, those games are compensation for price gouging. While it doesn't match prices elsewhere, Nintendo retains a customer and the first customer still paid full price (I passed the difference to him). Everybody wins. And I still got the club Nintendo points, although the items suck here.