OK, waffle, here's my opinion on your problem.
The wii,in general, takes some getting used to: knowing how far to be from the screen, how much to move your wrist, etc. etc. That said, the pointer used in LOZ is slightly more latent than in most wii games. Personally, I really don't find it to be too big a problem, especially when you consider that z-targeting will allow you to almost never need the crosshair. As for shooting into the ground, hold B longer before shooting. Or don't aim into the ground, whichever you were doing wrong.
I've said it before, but if you want proof that the wii can get over these pointer latency problems 100%, look at Trauma Center. The pointer feel like a laser pointer: no latency whatsoever.
So in short, after one gets used to using the wii, any control problems can almost certainly be blamed on the game, not the system or the remote.
Edit: i was writing this before chojin posted his post, which is why I repeated some points.
