First off, the new FF game for GC supposedly sucks really bad. And that's coming from the Japanese market
Secondly, Nintendo, well, actually, Miyamoto, came to Hideo and asked if he would like to make a MGS game for Gamecube. Since Miyamoto and Hideo are great friends, not to mention that Miyamoto is Hideo's mentor, he said yes. Of course, he only wanted to do a remake of a current MGS game, since he is against putting the series on other consoles besides PS2.