The addition of creep to the mod helped alot with balance although there is still one big issue. The population limit needs to be high to facilitate expansion but a problem arises because the hive player can zerg rush the enemy base after a hour or two with 1000 aliens and no amount of gun turrets can save you from this. Perhaps to mitigate this the population limit can be a function of the evolution percentage*max pop. with a minimum value for the max pop of lets say 20 or so aliens. This would give the player a chance to have defenses that could deal with the zerg given that evolution rate generally scales with the players progression. Its not a perfect idea and may be flawed fundamentally but I thought I'd give my suggestion as this is a awesome mod and I think it has countless hours of playtime potential. But to have 500+ medium biters attack your base when you don't have flamethrower turrets yet is a bit impossible. I hope you consider my recommendation.
Sincerely, TobuBiguru