There is a difficult balancing act involved in getting the most use out of the custom assets/systems created for a game, and overusing them to the point of wholly blunting their effect.
I was listening to Scott and Jorge discuss Call of Juarez: Bound in Blood and thought their comments on the quickdraw shootout system/scene were quite interesting. The game attempts to simulate the quintessential western high noon, staredown shootout (like this). And while it's interesting to watch and play once, as I did playing the demo, Scott and Jorge comment upon its impact quickly turning negative as more quickdraw events occurred and became increasingly difficult.
Implementing that quickdraw system was likely a significant undertaking. While I would applaud Techland for using it only once or twice during the game, I can understand the thinking that doing so wouldn't be a good return on investment. Unfortunately, trying to maximize the value of that particular system by increasing its repetition is problematic on two fronts.
One, it's not really in the spirit of the fiction. The staredown at high noon is a climactic event and usually incredibly slowly paced. The end of The Good, The Bad and the Ugly or Once Upon a Time in the West would not be nearly as impactful if there were showdown scenes at thirty and sixty minutes in as well. Call of Juarez: Bound in Blood attempts to make their showdowns poignant, but given it can't really be a climatic if it happens again and again.
But even more than seeing so many different quickdraw showdowns, is the problem of seeing the same one over and over if you fail. The wow moment disappears basically on the second go, and patience for most players wears thin quickly. Even if someone manages to push through after failing a handful of times, they're absolutely not going to have the experience that scene was meant to create.
In general, bosses in games are meant to do something similar. Provide special, climatic moments. But like Call of Juarez's quickdraw scenes, it's very easy for them to become the opposite of what was intended. After finally defeating the last boss in Metroid Prime, I didn't feel triumphant, merely exhausted.
Even recently, I've had these same issues with the boss battles in Little King's Story. The boss fights are tremendously imaginative and every one is very unique, but they're also pretty hard at times. And their cleverness and charm wears out when you've lost the King Shishkebaboo fight half a dozen times. Being enraptured by the game (if you hadn't noticed) means I can press on, but those moments aren't as gleaming as they should have been.
I understand the desire to get the most bang for developer buck. I also understand the additional challenge posed by so many people not finishing games. If you save the big awesome thing for the end, maybe half of your customers will even see it. I don't think there's any one solution to this issue. Shorter games might help, if that's a possibility. I'm sure far more people saw GLaDOS than the ~50% that saved the missile silo from the Combine at the end of Half-Life 2: Episode 2.
More orthogonal challenges, rather than ones that simply increase the difficulty of a known mechanic, might be another way to address this issue. I met Scott Rogers after his talk at GDC last year about level design and Disneyland, but his talk about designing enjoyable boss battles is renowned. Failing to mention it here would have been a grave omission indeed.
Obviously there's a whole lot going on with boss battles and there's been a ton of ink (bytes?) put down about the issue. I just thought it was interesting how Call of Juarez shared many issues in their quickdraw scenes, as have other games attempting to accomplish something similar. As is so often the case, if the design isn't treated with great conscientiousness, the end result can be the exact opposite of what was intended (and quite possibly worse than the thing being absent entirely). Proceed carefully, and test often. I don't think any player wants to find themselves in a mash-up of Tombstone and Groundhog Day.