Probably the most common complaint I've heard regarding TFP is how boring and uncharismatic Optimus is. and honestly, I quite agree, the dude is probably the weakest link in an otherwise brilliant cast of characters. At first, I had always figured the numerous cases of blandness and insubordination from his troops was simply due to deficiencies in the writing or Mr. Cullen's voice acting or direction, but after Ratchet's outburst at Prime, I'm starting to wonder...maybe he actually isn't meant to be all that great of a leader. As mentioned, his troops, particularly Arcee (who's meant to be his second in command), frequently disobey him. Further, he seems incapable of exercising any discipline on his human wards, and whenever he tries to provide emotional or moral support for his troops, it often feels cold and distant. With all that in mind, I think that there is at least a possibility that this is all deliberate. Maybe in the TFP-verse, Optimus was a once great leader who is no longer at the top of his game. His troops might still follow him out of loyalty, but the great big elephant in the room is that he simply isn't the leader he used to be. Again, Ratchet's outburst seems to hint that those might have been his hidden thoughts, let loose by his lack of inhibition caused by the synthetic energon.