I believe that the Zelda series needs to stick with the boss battles. But they need to be improved...A LOT. Skyward Sword was a step in the right direction but theirs still some room for improvement. If there is going to be a epic fight after a puzzle filled dungeon, then it needs to be... well epic.
I like what other people of posted, why not combine some of the ideas here? Such as you get to the final room which has a huge puzzle to solve. But here is the twist, completing the puzzle releases the boss which precedes to destroy the temple. So you have to flee and try and make it out of the falling apart dungeon by using your items. (Such as the bow to hit a switch, or the Hookshot to cross a newly opened gap in the floor) Afterwards depending how late in game this dungeon takes place, you would either fight the monster outside the dungeon, or the beast would be killed from knocking the temple down on itself.
I like the first option better but it could work either way. I think every boss battle should had something like this, not only to make it a epic fight, but so that you remember the battle (Fondly) after you win the game. I'm not saying you have to always run away from it, just something fun and unique from the last boss fight you had.