One possible reason for Ironhide losing his Jerk Jock streak over time may have had something to do with a shocking realization that he was pulling pranks alongside a 'bot (Wasp) who, by the end of the '"Autoboot Camp" was (falsely) incriminated as a Decepticon spy.
The concept of "electronic paint-jobs" works well with explaining why Transformers turn gray when they go offline; the paint-job is maintained only as long as they live.
Word of God is that the Autobots are a labour force while the Decepticons are a military force- and thinking about it, they were probably literally made for these niches. Our main Autobots scan emergency and rescue vehicles (well... kind of. Prime has no engine but he uses flame retardant hoses, and 'bee is technically a police car) while the 'Cons only choose military vehicles. 'Cons have superior firepower, but the Autobots have superior engineering skills. Kind of squares up with Sumdac's insistence that his company does not build war robots.
While we're at it, the "public protector" aspect of the Autobots is kept by the Elite Guard - many of them take cues from classic superheroes. (Magnus Hammer? Sentinel's shield? Rodimus is effectively a big metal Hawkeye).
In the two-parter "Human Error," Sari, upon receiving a motor-scooter that transforms into a backpack, says "I was kind of hoping for something with four wheels." Being part-Cybertronian, this indicates she wants to scan an alt-mode.
Some were confused when it was revealed that Bulkhead was an expert on Space Bridges and why it was never brought up earlier. Well, it could have been done earlier; IF in Episode 1, the Autobots didn't find the All-Spark, Bulkhead could have done something with the space bridge and showed his prowess with them long before. He wanted to be a Space Bridge engineer and likely studied like crazy to get it right.
Or it could be the fact that the team was clearing rubble in the first episode, rather than needing to carry out any mechanical repairs to the Space Bridge.
At the end of the series, Sari decides to travel to Cybertron to learn more about her Cybertronian heritage. Cybertron, at that point, is technically still led by Sentinel (acting) Magnus, who is so biophobic that he viewed Blackarahnia as an abomination-mockery of the Autobot she used to be. How do you think he'll react to discovering what Sari actually is?
In Wreck-Gar's official bio, it explains that he watches a lot of TV, and believes everything in the internet is true. As in the Transformers Wiki, how he does this in the bottom of the ocean makes you wonder, unless he can access the internet in his internal memory as the live action Optimus said they learned various languages in the internet, including eBay.