Question: I've been doing some reading about the people building an emulator for the Wii and it seems that given that it is nothing more then a beefed up GameCube, or the Nintendo64, so what makes build emulators for these systems so hard?

On a slight bit of a side note the hardware for these systems is surprisingly low:  

Wii:  

   729MHz PPC CPU  

   88MB Memory  

   243MHz GPU  

N64:  

   93.75MHz CPU (64-bit)  

   4MB Memory

Answer: 
Writing emulators is hard because you must exactly/completely/absolutely replicate said hardware behaviour, including it's OS behaviour in software.

Writing emulators for older consoles was in some cases harder than writing emulators for modern consoles. Because, a lot modern consoles use some form of Linux or \*nix so once the hardware is emulated software is a matter of dumping the machine's bios and handling over control.

Older consoles did everything in hardware, which means that reverse engineering played a much bigger role. You needed very good low level hackers to help you document how the old console worked and what each magic number meant.

Today, there's less magic numbers but instead standard GFX cards and CPUs. Although modern hardware has a lot more instructions and shiny doodads to emulate. A lot of what the more modern consoles do is well documented, unlike older consoles.
It is just because the game program is written for that particular hardware so it can utilize its all of the hardware benefits. Even if you have a super computer it cannot run properly a particular programs which cannot communicates to the hardware of the super computer itself. The same situation if you run PC games on consoles such as PS3/4 or xbox One. The only emulator that works 99% is Snes emulator and PS1.