I think the responsibility lies with Nintendo in as far as Nintendo seems to be the company that tried to get the deal in place, and Nintendo stood to benefit the most, so the Nintendo should have had a plan in place for marketing the game. I agree that Nintendo shouldn't be required to advertise 3rd party products, but if it's making deals for exclusive game releases, Nintendo has a vested interest in marketing the game.
Of course Konami has an interest too, and I think some of the responsibility lies with Konami, because it probably could have made a lot more money from the deal if it had spent some cash on advertising. I think the game's sales could easily be near half a million units with proper marketing.
Anyway, I don't think placing blame now does any good. If Nintendo does deals like this in the future, I think it should consider putting a marketing plan in place from the start that requires the third party to show a certain amount of support for the game in terms of advertising dollars, and Nintendo could agree to match whatever the third party spends. I think it's the responsibility of both parties to make the game sell. Nintendo wants it to drive hardware sales and show people the kinds of games the system is capable of, and the third parties (should) want to make money from the game.