Why implement microcontroller in FPGA?
If your project is going to use an FPGA for the grunt work, and it has the spare capacity, why would you go to the expense of an extra chip when you can just implement it in the FPGA?

For many procedural control environments it can be considerably easier to implement the required setup in a language like C than trying to do it in VHDL or Verilog.  By adding the microcontroller into the FPGA you get the best of both worlds - the power of the VHDL / Verilog etc for the logic and interfacing systems, and the simplicity of a procedural language for the core control and management systems.