Nothing more appropriate to this third release than a firmware that can handle 3 controllers:

The firmware can work with either controller and will report buttons in the following sequence:

Besides the Arduino Micro, only one component is required: A DB-9 male connector:

The prototype was assembled on a proto-board:

Pin:  9  6  4  3  2  1
Sel=0 ST A  0  0  DW UP
Sel=1 C  B  RG LF DW UP
 

When the 6 button controller was introduced a similar problem showed up and this time the solution adopted was very peculiar. Another Mux was added inside the controller for the extra buttons and the control of such Mux is triggered by a counter that in turn is activated by the "Select" Line. After the third edge the extra mux is activated and the buttons X, Y, Z and MODE are present on the data lines. But one problem left (again). How to synchronize the game code with the pulse count? Simply counting the pulses issue is out of question since the controller can be inserted and removed while the game is running.

The solution for the six button controller used two mechanisms:

The first is to generate another invalid pattern, this time with all directionals activated at the same time right before the extra buttons ( X, Y, Z, MODE) are ready to be read. Additionally, all the directionals are deactivated on the next edge after the extra buttons are read so the game can differentiate between the "all directionals activated" from "all extra buttons activated".

Pin:   9  6  4  3  2  1 
Sel=0  ST A  0  0  DW UP
Sel=1  C  B  RG LF DW UP
Sel=0  ST A  0  0  DW UP 
Sel=1  C  B  RG LF DW UP 
Sel=0  ST A  0  0  0  0  -> Directionals LOW right before extra buttons 
Sel=1  1  1  MD X  Y  Z     3rd rising edge
Sel=0  ST A  1  1  1  1  -> Directionals HIGH right after the extra buttons 

The second mechanism is a timeout. It the Select line do not change state again within ~1.5ms then the internal counter is reset.

The code performs a series of samples and checks the state of the unique conditions to identify whether the controller is a 3 button or a 6 button controller. If neither one is identified the code assumes that the controller is a Master System (or unknown)

uint8_t SEGAscan(void) {
  uint8_t sample[7]; 
  uint8_t type;  
  combinedButtons = 0;

  sample[0] = readController();   //  ST A  0  0  DW UP
  
  digitalWrite(genesisSelect,HIGH);   
  sample[1] = readController();   //  C  B  RG LF DW UP

  digitalWrite(genesisSelect,LOW);  
  sample[2] = readController();   //  ST A  0  0  DW UP 
 
  digitalWrite(genesisSelect,HIGH);  
  sample[3] = readController();  C  B  RG LF DW UP 

  digitalWrite(genesisSelect,LOW);   // 
  sample[4] = readController();  ST A  0  0  0  0  

  digitalWrite(genesisSelect,HIGH);  
  sample[5] =  readController();  //  1  1  MD X  Y  Z  

  digitalWrite(genesisSelect,LOW); 
  sample[6] = readController();   //  ST A  1  1  1  1 

  // check for 3 or 6 buttons
  if ( ((sample[4] & 0x03) == 0) && ((sample[6] & 0x0f)==0x0f) ) {
     type = _6Button;  
  } else if  ( (sample[6] & 0x0c) == 0)  {
     type = _3Button;
  } else
     type = _unKnown; 
...
...
}

The rest of the code uses sampled data to form a 16 bit word with the state of all buttons, as applicable to the type of controller.

  // now populate combinedButtons variable accordingly       // 15 14 13 12 11 10 9  8  7  6  5  4  3  2  1  0
  combinedButtons = (uint16_t)sample[1];                     // 0  0  0  0  0  0  0  0  0  0  C  B  RG LF DW UP
  combinedButtons |= ((uint16_t)(sample[0]<<2)) & 0xc0;      // 0  0  0  0  0  0  0  0  ST A  C  B  RG LF DW UP
  combinedButtons |= ((uint16_t)(sample[5]<<8)) & 0xf00;     // 0  0  0  0  MD X  Y  Z  ST A  C  B  RG LF DW UP
...
  // invert bits. Make '1' the active state 
  combinedButtons = ~combinedButtons;
  switch (type) {
    case _6Button:
      combinedButtons &= 0x0fff;
      break;
    case _3Button:
      combinedButtons &= 0x00ff;
    default:
      combinedButtons &= 0x003f;    
    } 

And that concludes the third release.