I always thought him to be conscious to a point during his imprisonment, or at least for a good segment of it. When he breaks free and shouts, "I am Megatron!", it didn't seem like a generic declaration to me.

Makes more sense that it was a correction to the humans who had been calling him NBE-1 for decades than for it to be a reaffirmation of his identity. Notice, too, that he said it in English. He got the language real fast off the web, or he picked it up over years.