I see quite a few parallels between Animated Optimus and BW Optimus. Both are new to the leadership role, and as such, are only in command of a small team on one exploration/maintanance vessel. Both Optimus' are still yet to earn the loyalty of teams at the time of their arrival on Earth. Both tend to rely on a veteran of the team as a crutch, while having trouble in getting the rest to follow his orders.
The main difference though, is that Animated Optimus actually had military training (the amount is still yet to be disclosed), which should make him a more capable warrior, but his lack of military experience (like BW Optimus) is his flaw, so he doesn't yet have the confidence to tackle the Decepticons, or have the reliability of his subordinates following his orders without question.
I think the flaw of the Animated series is that it is being written too heavily for 5-8 year olds, so the behaviour and characteristics of the cast reflect the behaviour of that age-group, to make it easier for them to relate to what they are watching. Misbehaving, disrespectful, sneaky - concepts young kids can relate to, so unfortunately the 'integrity' of the Autobot name is being corrupted by the Animated writers just to get ratings.
I'm disappointed that Animated Optimus hasn't yet 'got a pair' after 15 episodes, and don't hold out much hope that he ever will if the upcoming storyarc pertaining to 'other Autobots' has him running around as a subordinate himself (I'm guessing this - it is not a spoiler).
At least BW Optimus had his moments when he would just snap, take charge, kick butt, and save the day.
It's not surprising that Animated Optimus hasn't really had this sort of moment, since most episodes so far haven't involved more than one Decepticon (if any), to threaten them.