Top down perspective.. awkward?
Maybe if you're a little kid and didn't grow up on the things..
You can't see things that are more than 20 feet away (I know I'm quoting Yahtzee here). That's a giant flaw when you fight enemies with ranged attacks. Link to the Past had a few of those. The only advantage was seeing around walls.
Personally I think the wiimote controls of TP are pretty intuitive.. swing the remote in any direction, it swings the sword.. have a bow drawn? Point at the screen where you want to shoot and shoot, shield bash by thrusting the nunchuck forward.. the only somewhat awkward move is the spin attack which you do by shaking the nunchuck side to side a few times, sometimes it takes longer to register than others.
I grew up on console controllers with D pads, and joysticks, and I still find the Wiimote to be a better control input.
Oh yes, the wiimote seems intuitive... until you try to move. Movement itself is the wiimote's big giant flaw. The motion sensor is also a bit buggy, but it is for most so I can't really hold that against them since the technology, while impressive, isn't where we want it to be. Of course Zelda and indeed any game that has another console port will tend to suffer from this problem.