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I really love Kojima for this, many bosses are but in there as a story moment to Warf you down and show you just what you have to build up to fighting. But on NG+ or if you just are really fucking amazing some of those intended to lose battles can be won and the boss will react appropriately like "WHAT?! IM GETTING THE STORY GUN NOW HOW DARE YOU BEAT ME BEFORE I CAN MONOLOGUE BALWAKJLAHKLWA" and even say so on the following events like "YOU WONT BEAT ME WITH MY MCGUFFIN". But yeah I'm so sick of the 'have to lose to this guy so you have a grudge, trolololo' mechanic too.
And MGS3 gives you a chance to shoot the third boss before you've fought the first boss.
I loved the end, you can also beat his whole fight by waiting like a month between saves and he dies of old age. The exploding wheelchair though where you can just rando snipe him was beauty.