Metal Gear Solid 3 to me is what Metal Gear Solid was but doubled. You have some brilliant stealth elements brought into play, CQC; a new factor that helped evolve the game further, changing camo, this is truly the pinnacle of stealth action. Not to mention the epic feel of the 60s that makes you mark out to the James Bond-esque intro, brilliant story that adds more depth to the MGS world and the boss battles were challenging and really upped the game, the battle against The End is a perfect example of a Sniper battle, this even trumped the battle against Sniper Wolf in the first outing.
Banjo-Tooie is a great game, nothing to take away from it, but it does have its flaws and this is Naked Snake's to lose here.