Yeah GameCube was the least of the Nintendo consoles, software wise.
If all are included then GameBoy Advance, 6th Gen was just a 'bad' Gen really. I never played Virtual Boy though, since that wasn't released in Europe. I'll get one some day though, just because. Both the GameCube and the GameBoy Advance are the only ones I don't play anymore and are both the only ones that are neatly stacked in their boxes. I rarely play GC games and when I do, it's on Wii, same with GBA games, which I play on DS.
Don't get me wrong, 6th Gen still had it's moments. In fact, my number 2 game of all time is 6th Gen.
The Wii is better than GC, and the DS is better than GBA. The WiiU and 3DS are looking to be better than those, so I'm glad Nintendo found it's way up again!
Doubt there will ever be a N64/GameBoy Color-like generation again, but that Gen is pretty much unbeatable quality wise if you asked me.
@spurge: To add to all the help, if you suspect there are areas out of sight, or that you've missed, never forget the Dowsing option!
Even if there isn't a dowsing option that's directly what you need, you can dowse for something that's most likely there, like hearts or rupees (though you probably don't have that one yet). And like TripleMMM said, the map reveales a lot of secrets when examined more carefully.