I agree with you MajorasWrath1, that it was a huge miss of Nintendo to make the Water Temple have this glitch. If anyone doesn't believe me, here is the You-Tube instruction video, if you still don't believe it, try it for yourself, because I did it!!!

YouTube - Legend of Zelda: Master Quest: Skip the water temple

Also, I'm adding a poll to this thread:

Master Quest is:
Easier then OoT
The Same as OoT
Harder than OoT

So everyone please vote.

I pretty much agree with you ZAR, did you especially find that with the Fire temple you had everything you need to defeat the boss, like half way through the actual temple?