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: 
There are a number of reasons why emulation is difficult.

1. Emulating a system requires a lot more power than the target system

Sometimes the host system needs an order of magnitude more power (speed) than the target system. This is easy to understand if you consider the host machine needs to do all the work of the original system *and then some more* work to manage all communication between components while also sharing the system resources with other applications. This is why it takes a 2GHz processor to faithfully emulate a SNES which runs at a measly 21MHz. 

2. Sometimes the instruction sets and/or subsystem workings are unknown to people

Most hardware is essentially a black box and understanding how it works is figured out through reverse engineering which takes a lot of time and patience. Not to mention, companies try their best to make reverse engineering difficult and companies have gotten much better at this post Playstation 1 era. 

3. Lack of people building emulators

Emulation is a pretty niche area that requires a lot of working knowledge in many domains. To be frank, there's not a lot of people capable of emulating many of the modern systems. Emulating these systems takes a lot of time and effort and only the most dedicated will actually do it.
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.