I want to add "Garbage In, Garbage Out" in that list of "fun factor". That episode makes me laugh every single time I watch it. It's absolutely wonderful. Wreck-Gar is hilarious, Looney Tunes in his own way while fitting in the TFAverse. The episode even doubles up by giving Ratchet more character development.
I'm going to be a fangirl and add Prowl to that list. Much more subtle on his end, but Prowl's fascination for humans is expanded here after gaining appreciation for them after Fanzone impressed him back in Season One ("Survival of the Fittest"). A very nice throwback. Also, human Prowl and the baby - adorable and gut-wrenching with its foreshadowing ("I'm just thankful to be alive in any form.") Oh, you cheeky writers.
That said, while I adore both "Human Error" and easily consider it one of the crown jewel of Season Three (which, unfortunately, is my least favorite season), I honestly think this is something that could have been cut to just one episode. The first part already structured it very well: Autobots become humans, they explore their new bodies, they find out it's all an illusion, and at the last stretch, they could have stopped Virtual!Soundwave, get back to reality and whoop the real one, too.
The second one just feels like an unnecessary extension. Yeah, it gave Sari much needed camera focus after being absent for much of Season Three prior, but hers is a story that needed to focus on her robotic half, not whether she is equipped to be leader. Also, even if they went that direction, I honestly think the Substitute Autobots could have carried a separate, unrelated episode on their own. They each interact wonderfully and adds a lot of humor to the episode (like I said in the list, TFA is really, really good with character interaction) and heck, it's the only time I ever liked one of the Constructicons. Either way, the second half was unneeded in the grand scheme of things that Season 3's list of unanswered questions should have worked on instead. Cancellation, what are ya going to do?