Dang that's pretty sad that idea was abandoned... all well. Also great suggestion, been a fan of that game for a good long while, still play it on occasion.
Well... from a game play mechanic perspective I can understand why male as a possible gender got taken out. Unless Mado was interested to do some possible bishounen/trap/yaoi action with this new game (which I assume they don't judging by their previous games), adding only one in-game male character to represent the player would only limit how much can off springs be produced with one character.
Could have been an interesting idea to bottleneck the player's manpower/economy growth if a game is set with only a single male character to impregnate a vast pool of randomly generated female characters. But I'm guessing in the end Mado didn't want to turn this into a 'plug in the math formula game', so that idea got dropped very early on during development.