Kojima left them alone and they fucking trainwrecked it.
It was so bad that Kojima had to go to Platinum with hat in hand and basically beg them for help. I'm sure that was a harsh lesson for Kojima that his team is indeed not capable of making a game without his supervision; something he tried to accomplish before even MGS3 was released. But similar to Rising, MGS3's development was a mess and he had to step in.
They took on a brand new genre (to them) with an interesting game concept. The reason why they floundered was because they struggled with designing a game in which you can 'cut anything'.
I haven't heard much about their MGS3, but Rising had the odds stacked against his team. It's reasonable to expect them to fare better making a standard Metal Gear Solid stealth game, like a big-budget heavily staffed Portable Ops.