The difficulty of any particular boss should be based on how far the player has progressed in the game. Much like schooling, one would expect each subsequent year to be more challenging than the last; one would expect High School to be more challenging than Junior High and College to be more challenging than High School. It is by this same logic bosses should progress in their level of difficulty. Today, especially in games like The Legend of Zelda Phantom Hourglass, boss battle difficulty remains rather static, even up to and including the final boss. Using the Legend of Zelda as an example, I truly believe the single best Zelda game in this regard is Majora’s Mask. Each boss increased in difficulty, ultimately leading up to an extraordinarily challenging battle with Majora’s Mask (if one did not use the Fierce Deity Mask). In a way, each battle was like a "final exam" of sorts for each form Link could take in Majora’s Mask (Deku, Goron, Zora, himself) with the addition of other items obtained from throughout the game. As those of you that played Majora’s Mask can attest, each battle does increase in difficulty and scope. It’s battles like these which are missing from the modern gaming era.
However, even with difficulty, it is important to balance difficulty a bit so less skilled players still have a shot at making it through. The Adventure of Link comes to mind; making battles which are simply absurdly difficult serve only to frustrate the player, making them less inclined to improve their skills and try again. A number of factors contribute to this level of difficulty, including lack of player skill and the unpreparedness of the player’s in-game character to take damage or perform the skills necessary to win the battle. The Legend of Zelda has never really had an issue with the later, with the exception of The Adventure of Link, but it’s important to note to prevent such things from making their way into the games to begin with. The former, the high level of skill necessary, is a bit more difficult to follow. Difficulty is really something that needs to be balanced; it’s similar in a sense to a thin line between easy and hard. A great battle will make use of this line, at all times. As mentioned before, this line should move slightly more to the side of "hard" as the player progresses, but moving too quickly is grounds for disaster.
Honestly, on the whole, The Legend of Zelda has done a fantastic job with boss battle difficulty over the years. As a matter of fact, it’s one of the things that makes Zelda, well, Zelda. However, especially with some form of "new Zelda" to be displayed at this year’s E3 Expo (or so we hope) one can only hope that Nintendo will continue down the path of the true Zelda fan rather than attempt to cater to the less skilled player.