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design idea for micro controller

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I went through a similar exercise. Once the design was finished, I didn't feel the need to build a controller because the ready-made ones were better than the one I could built, but going through the exercise taught me a lot.You can start with a simple example

For a basic microcontroller you need to have some program memory, one of more data registers, one or more address counters/registers and some sort of arithmetic or logic processor, which could be as simple as the 4 bit CD40181 ALU. An instruction register (latch) can simplify your design greatly.

It would be best if you studied some existing controller instruction sets (PIC is a good start) and understand how the elements above would be connected via the instruction set, then whip up something simple that could execute those commands. 4 bits of data, 4 bit instructions, no data RAM, low clock rate. Upon getting it to work, you will be a computer architect.
 
A functional design is a block diagram that shows what each section does, and how and with what control signals go from block to block. A logic design would be the actual hardware used to implement the functional block.
 
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