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.
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.