Reception of Season 2 overall: Even better than Season 1! More positive reviews, and no negative ones. The 'complaints' Volk-Weiss has noticed seem to be mostly wishes for even more content or depth, which he understands and sees it as a good thing that these are the biggest complaints about the new season.
Biggest challenge in making the Transformers episode? Some former Takara engineers were new to being interviewed, so that initial footage wasn't very good. According to Volk-Weiss many of them later grasped the idea better, and took their own initiative to re-shoot better interviews.
Why a lack of more "in-depth" material about Transformers? The Toys That Made Us aims for a "middle ground" sort of approach to their episodes; some things that fans might find interesting would lose non-fan viewers. This is why some things exciting to fans were glossed over, and why only Peter Cullen (arguably the most "iconic" Transformers actor) was interviewed for the episode.
Any cut material you wish you could've kept? The original cut for the Transformers episode was 90-100 minutes long, and among cut footage was an eight- to nine-minute segment on Beast Wars. Mentions of much of this cut material potentially being available on a DVD of the series, if/when that comes to pass.
An interview with Michael Bay was also filmed, but wasn't included in the final cut for various reasons, which Volk-Weiss can't elaborate on further (though he stresses that Bay was fantastic to talk to and nothing went wrong in the interview).
Season 3: Volk-Weiss hopes to end up getting to make around 20 episodes! The chances of, in those 20 episodes, coming back for another pass at a brand (like say, Transformers) are estimated at "0.001" but it's not impossible. Subjects for Season 3 will be revealed at The Toys That Made Us panel at San Diego Comic-Con... it's hinted that Power Rangers and Gundam may be among them!