Legend of Zelda, Twilight princess. About the time I got to the water temple, I stopped, then realized that instead of curiosity and a sense of wonder about this new stage, I was feeling a sense of dread, thinking, "Oh god, what incredibly monotonous, bullsh*t puzzles await me in here?" and just stopped playing. I was no longer exited by the thought of exploring and finding things like heart pieces, but absolutely dreading it.
Don't get me wrong, I love the LoZ series, but despite even changing Link into a bad-ass wolf, and giving him an awesome Navi-replacement, it still, felt, the exact, same. You could have replaced everything with zombies, Hitler, ninjas, and Duke Nukem, and it still would have felt unmistakably like a Zelda game.
Also on that note, Beyond Good and Evil. Why? Well, first off because I got stuck in a dungeon when I had to, you guessed it, find a series of switches and fetch-quests to "solve a puzzle" to activate an elevator and get through the level, despite the fact I had already explored every nook and cranny and killed every enemy I could find. Add that, to the "Pearl orbs" or whatever you have to "find" in just as precarious and downright annoying spots as heart pieces, and you can just slap the "Legend of Zelda approved!" sticker right on there. Though I am still haunted by the thought that maybe I gave up too early...
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Another runner up would be Starwars: Battlefront II for PS2. I think it was at the point where you take over the rebel ship, reenacted from the beginning of "Episode 4, A new hope." The rebels have, literally, infinite guys, on their tiny ass ship, and you only have about 30 before the mission is failed. That's about where I called BS on the whole thing, but somehow stuck with it until I got to Hoth stage. Oh...my...god...You know, I don't exactly recall having ten million guys on my side when I was the rebels in EVERY OTHER STAR WARS GAME EVER...