Intensity of the graphics is only one factor. Remember, the bottleneck in Gamecube emulation is the CPU, not the graphics. So, scenes in which a lot of work has to be done by the CPU will suffer.
For example, in Wind Waker when you're outside on an island, emulation slows down a lot. Let's think about why this happens. When you're standing outside, the entire map tile is being actively processed by the Gamecube: Somewhere, there's a map-drawing fish jumping around; somewhere else a flock of seagulls is flying; somewhere else there are some sharks waiting for you to find them; somewhere else a pirate ship is looking for a hapless victim to shoot bombs at; and who knows what else is going on on the island itself. All of this needs to be managed by the CPU.
Now, enter a house and emulation speeds up. All the CPU has to think about now is what's going on in the house, which usually doesn't amount to much. Compare a battle on SSBM to that, and it's understandable why it would be fast. The graphics may look nice, but overall, what's going on is relatively simple: Up to 4 characters move around the screen trying to hit each other with attacks. Not too complicated compared to the processing that has to go on in some other places in some other games.
Granted, that's an overly simple explanation of why it works the way it does, but you get the idea: More stuff going on = slower emulation.
