I completely agree that nuking was the most logical choice. And arguably the best ending, but I disagree that Kyle would have made the choice. Especially in the very, very short time frame that he had to make the decision. A great example is that while infiltrating Rais' compound on the mission The Pit the GRE has been replaced and it is told to Kyle tht they are going to carpet bomb the city. He reacts emotionally and curses them. He reacts the same way later in the game as well. Kyle's reaction is clear. He simply wouldn't just give up and nuke himself and everyone he cares about without at least struggling with the decision. Unless the argument is when confronted with the reality of hyper-intelligent volatles he spirals into a deep well of depression and simply gives up. I can accept this as an answer but I think this depression should have manifested in some dialogue or a last minute attempt to contact the tower.

As for the gas (I should note Its been some time since I competed the game and don't remember everything about it) even if it was a milliary creation it poorly explains why it has such drastically different effects on the population. Likewise it seems dissonant that Kyle got lucky and became a sentient volatile where as the majority are not. I would like to also say that it seems unlikely that the mother would be the only other sentient volatile if the gas really had this effect. She surely would have turned others. The military probably tested it right? Where are those volatile. It just seems too damn unlikely.