n my understandings, It's more of "nintendo let SK go" not "SK doesn't want to work with nintendo"
The (sad) fact is, SK didn't sell many games, despite how amazing talented as a devoloper they are. They weren't really making a profit. When MGS:TTS was first announced, I saw it as a last chance for SK to make a profit to cover from the ED losses. I'm not entirely sure about this, but apparently MGS:TTS didn't sell nearly as well as hoped.
Nintendo, being in the business for money, probably was like "SK, we love you guys and all... but you just aren't making us any money". Which is probably why SK is now free to develop for more than just nintendo.
At the very least, SK now has a better chance to survive, I personally don't care if a title is no longer Nintendo-Exclusive, As long as SK can stay in business and continue making games, im fine with whatever choices Denis has to make.
You have to remember there are 2 points of view here, Nintendo's and SK's.