I agree with part of Yahtzee's last statement. The Metal Gear series can't start laughing at itself now.
It can't start laughing at itself now, because it's been laughing at itself for years.
Case in point: MGS3. Not that I'm suggesting that it only started pointing at itself around that time, but it's just the easiest one for me to find examples in. To stay on the subject of Raiden, how about the many, many jokes at his expense involving the the easter-egg opening with the Raikov mask, Raikov himself, and the Snake Eraser video? Outside of that, we have SigInt seriously questioning Snake's fetishistic fascination with the cardboard box, a man whose super-power is being covered in bees, the theme music blaring over a particularly long ladder-climbing sequence...