Why are people so upset? Nintendo clearly stated this is their new strategy at investor meetings, they won't let that game go.
Nintendo doesn't just invest in a single game. They do this to build up a long-term relationship. Look at Capcom and Monster Hunter or Square and Dragon Quest or even Team Ninja and Nintendo right now. Nintendo had no chance but to pick specific third parties and start close partnerships with them - they didn't get the support they wanted this generation but 3rd parties are vital to any platform.
So far we've only seen Nintendo advertising or publishing 3rd party games which, apparently, was enough to convince developers to collaborate with them. Now Nintendo is stepping that game up by actually funding development. Get used to it: This is Nintendo's new strategy and it was discussed countless times at investor meetings. This will happen frequently in the future.
I wouldn't be surprised to see 3rd parties develop games with Nintendo IP's in the future (like F-Zero GX or Starfox on Gamecube).
Again: Nintendo does this to build up long-term relationships not to pump out single games. They won't let those developers get away that easily and will try to deepen the collaboration. And it looks like those developers like what Nintendo does.
Edit: Super Smash Bros + Namco and Metroid + Team Ninja, Level 5 and Layton / Inazuma (Nintendo publishing those games in the west) are more examples of this. And there certainly are more of those collaborations we haven't heard about yet because the games are not yet ready to be shown. I also wouldn't dismiss the rumours of Nintendo trying to buy back Rare because of its IP's. This is Nintendo's current strategy and they openly talked about it.