They're a big part of it (especially because they're the only new characters that recur regularly), but it's more the repetition of stuff they covered perfectly well in Season 1. In S1, the Autobot Learns a Lesson episodes were fine -- Bulkhead is clumsy and misunderstood, Ratchet is a cranky old guy who needs to work on his interpersonal skills, and Bumblebee is reckless and doesn't think ahead. But they all Learned a Lesson about that and moved on. It felt like a bunch of the episodes of S2 have to pretend that none of that character development happened or else they don't work. Ratchet is still Cranky Old Guy in "Garbage In, Garbage Out." Bulkhead is still clumsy and misunderstood in "Rise of the Constructicons" and "A Bridge Too Far Pt. 1." Bumblebee is the most forgivable, since it seems like it's part of his character to be impulsive and not to learn from his past mistakes, but even so, it seems like stuff in "Velocity" and a few others take that a bit too far. It's not that any of this is WORSE than season 1, but that it's the SAME as season 1 when the show should have moved past that. They're staying still or stepping backwards when they move forwards elsewhere.
And, as I said in the review, the Autobots are all turned into complete idiots in "Rise of the Constructicons" for it to work, and was anybody anywhere not able to figure out the Sari plot twist as soon as the words were out of Porter C. Powell's mouth? Why waste the time playing up that mystery when the answer is so painfully obvious?
Oh, and nowhere near enough Prowl. Forgot to mention that in the review.
Maybe it's that the highs are higher in this season, but the lows are much lower. The Elite Guard trilogy that kicks things off really is marvelous. The characters are smart and they learn from things (except Sentinel Prime, but the whole point is that he's a dense, arrogant jerk, so that's OK).
I do enjoy this series thoroughly, regardless of the little things that annoy me about it. I may even try to catch the regular broadcasts once season 3 kicks off.
-- Ed