I was thinking about the Square Enix statement today and something occurred to me. I thought it was very weird how he put it - "We don't want the PlayStation 3 to be the overwhelming loser, so we want to support them," he said. "But we don't want them to be the overwhelming winner either, so we can't support them too much."
Now I think I've figured it out: Square Enix isn't that afraid of Sony, it's afraid of Nintendo. I think it's clear that Square Enix doesn't see Sony as the sure bet anymore, but why is Square "we support the most popular console" Enix saying that it doesn't want anyone to be too popular, after supporting runaway victor Sony for ten years? Because Square Enix is scared of Nintendo once again becoming the tyrranical overlord of all video games.
Okay, so I do have an alternative theory: Square Enix sees Nintendo as the greener pasture, but after burning bridges with Nintendo over the N64, it doesn't want to do the same thing with Sony.