The Autobots were a huge army, but they've been scattered and reduced to working in small units, and sure, Ultra Magnus probably does need to adjust to this. But Wheeljack's immaturity really doesn't help. Here's a commanding officer who's out of his comfort zone working in an unfamiliar structure... work with him. Constantly disobeying his instructions and giving him attitude doesn't help anybody. And the show implies that Wheeljack's had this attitude for a long time, possibly even before the Autobots were diminished.

The problem with Ultra Magnus is that he's freaking inconsistent, and that irritates me greatly (especially considering that consistency is the core spirit of the Ultra Magnus character; just as fighting for freedom is the core characteristic of Optimus Prime). He's ineptness comes from his penchant for insisting that everyone follows the rules, but does nothing to enforce them! Rules are pointless if they are not vigorously and consistently enforced. Ultra Magnus is partially at fault for the way that Wheeljack treats him because he _lets_ him get away with it. The moment Wheeljack backchats Magnus his reaction should be, "How dare you address me that way!" and bloody do something about it! In this way, Megatron's actually a better military commander because he will suffer NO disrespect from any of his troops. He's even managed to get Starscream in tow because unlike other Megatrons before him, he refused to put up with Starscream's crap (Animated Megatron too - but his Starscream went and became undead/immortal... snap ). Megatron's soldiers follow his orders to the letter... it's little wonder that the Decepticons have the upper hand (and a miracle that the Autobots weren't wiped out centuries ago).

If Wheeljack has an issue with Ultra Magnus, he should be deferring the issue to Magnus' commanding officer, Optimus Prime. Then Optimus Prime can counsel Magnus and help him better lead the Wreckers. That's really what should've happened centuries ago back on Cybertron. But the stupid thing is that Wheeljack just up and leaves. It's just his whole stubborn "lone wolf" thing which works out to be lame because the story doesn't seem to provide any endearing reason for why he lashes out against authority (other than just being a tenacious punk). Depth Charge is an example of a better written lone wolf IMHO. He was provided with a far more credible back-story for his mistrust of authority.

"I've gotta hand it to you, (Optimus) Primal. When you screw up you do it big-time."
- Depth Charge [Deep Metal]