They should be both, but what kind of reward and what kind of challenge should be different for each game.
For example: The helicopter on the train in Uncharted 2 is a reward of spectacle. It's an amazing fight from a cinematic perspective. The sequence wasn't too difficult, but it did add a layer of complexity to the sequence that increased the stakes. If the helicopter wasn't there, it would just be Nathan running down a very long train for a very long time. The sequence would get boring. The stakes wouldn't be raised. The intensity of the sequence would not last until the end of the mountain range.
The helicopter part is a good way to raise the tension mid way through the train sequence. Once the helicopter is defeated, the cutscene is over, and you're in the tunnel, you breathe a sigh of relief and the gameplay can slow down a bit, only to rise and fall again naturally as you progress through the mountains.
The challenge was gently sprinkled on at that point, but it was enough to make the rest of the sequence around it better. Your reward was the rise in tension during the fight, the over the top cinematic action of the boss fight occurring on this moving train, the cutscene of the crash before the tunnel, and the satisfying drop in tension as you progressed to a much slower gameplay pace.
That's just one type of boss fight though. And it's a type of boss fight that works with that game.
Another example with a great use of boss fights both as a reward and as a challenge is No More Heroes.
No More Heroes is all about proving yourself. You have to slog through slow, monotonous side missions to get the cash to prove you want to progress the story. You then have to wade through cannon fodder after cannon fodder to prove you have the guts and skills to actually face the boss fight. Then, once you get through this annoying and frankly pretty bad gameplay, you're rewarded by the opportunity to prove yourself complex, multi-layered, incredibly challenging boss fights that are among the best that have come out this past generation. They are a reward for your patience and diligence. They are a test of your abilities, your reactions, and your problem solving skills (learning the way the boss moves, how they attack, and when you have an opening is half the enjoyment). You'll die. You'll get hit by moves you didn't see coming. You'll fight the same boss for twenty minutes and then lose because you hesitated.
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