Sounds not like a bad idea... if you play as a bottom then it won't matter much, but I think it still matters a lot more for dominant top players?
All the sexy scenes may change involving your dick size and that means a lot of (extra) (re)writing...
ooo what about a path changer that depending on the size of your penis it will decide if you become the bottom for the character(Logan) or you become the top for the character(Logan) XD
ah.. yeah I think that would still need some more extra writing... and I don't think Hyao wants to add more when he's finished the game :p