All of the devices you use right now have processing units that can be communicated with. They contain logic circuits. Imagine a bunch of lines on a piece of paper and the weird circuit/shapes/loops/connections it makes. Every type of processor has a different diagram of this.
If you send into the input areas of those circuits a certain series of signals (input some 1s and 0s), the circuit will manipulate these 1s and 0s into a different pattern of 1s and 0s that we know how to make sense of. Multiply this by a billion times and you can have very complex logic being processed by inputting very simple operations in small successions. (Check out logic gates on YouTube, look for the explanation with light switches and lightbulbs).
The circuits for these CPUs are set in stone (or rather, silicon) once they are manufactured, and you HAVE to communicate with them in the instructions that logically make sense for them to process. Every CPU ever has its own assembly language that manipulates, at the bit level, what operations it performs at certain memory addresses. All the other languages that are higher level (C, C++, Java, etc) are higher level abstractions of that assembly language, they all compile down to the same machine code for each target CPU.
The thing about this is, as you introduce newer CPU logic designs, you tend to lose compatibility with processing older instructions. Yes, your current computer has a processor a billion times more powerful than the original Game Boy, but you cannot take Pokemon Red's disassembled machine code and run it natively on your processor, the instructions won't make sense to your processor. The circuit diagram for the Game Boy, and as such, the "instruction set", or the vocabulary in which you can communicate with the CPUs, is likely very different.
At this point you may be thinking - But you can run Pokemon Red on your computer, through an emulator. You're right, that's beause an emulator (in context of the discussion here) is a software layer between the machine code of the Pokemon Red ROM that translates the instructions from old operations to the familiar operations of your target machine architecture (that's one way of doing it, called Dynamic recompliation - another way is to mimic the original Game Boy processor in software and feed the instructions to that, but big picture - there is translation going on). The reason for all that is that your current processor's architecture itself is not malleable once it has been created. FPGA will change all that.
FPGA enabled you to not program software, but to program hardware. The physical gates that create the logical circuit diagram of FPGA chips can be modified to create different circuits on the fly. If the technology can reach fully hardware programmable chips, the implications are huge.
Super simplified: In 20 years, you might be able to download a circuit diagram for the NEC VR4300 in a standard file format, load it up at BIOS runtime, and run an N64 game ROM with absolutely 0 emulation. It's like you 3D printed the N64 hardware; your CPU will T-1000 morph into the old CPU based on a logical circuit design description you can load into it.
