Of course not as the first weapon. As nuclear weapons are considered as most destructible weapon conceived by mankind, however, it makes sense to use them as example of "ultimate firepower". At least for me.
Exactly, the autobots. What I'm trying to say that it seriously sucks when mankind ends up completely useless, weak and pathetic in war against some stupid aliens. I mean, many things isn't cheesier than end of War of the Worlds.
Nothing can stop alien armada and then pufffsh - they all end up dead. Hilariously oxygen was fatal for them. Race with that level fo technology weren't capable enough to monitor what consists atmosphere of the planet they're conquering etc. ? Oh give me break. That's nearly as worse type of narrative like "then he waked up and everything had been dream" (Mamoru Oshii, I'm looking at YOU!).
This is not case in Transformers except in one way. Instead of deadly oxygen there are autobots. Mankind on its own has no chance.
X-Files is awesome, but it too fails into this terrible, one of the oldest cliches of science fiction, "invincible aliens" scene.
As a good example I'm looking at ents in LotR. Orcs were capable of bringing them down, but it was so hard task that they had pitiful percentage of succeeding in it. Situation however wasn't insta-lose for orcsies.