I have heard this a few times. When i personally watch Allen's college game footage verses Manuel's college game footage there is very little comparison in how they play the position.
In regards to swagger etc, Manuel did not strike me as having swagger or command of a room. He seemed genuine and nice and intelligent, but Manuel did not command respect from his team mates. I think Allen will.
Production ultimately is what counts. I do not think it is fair to compare Allen to Manuel or any other QB for that matter, including Kelly.