I thought the Water Temple was fine as is... I don't remember when I played but it was my sezond Zelda after MM and I didn't have trouble... I know at most I was 11... o_o
As for Navi, who will tell Link to see the Great Deku Tree? Not to mention those useful tips fighting enemies! Oh, and when she flies to a point where you have to play the Princess's Lulliby or the Song of Time (maybe that's why people had trouble? )