Watching Santo vs Dracula, I would say I would like to see more bot naiveness.
When they ask the host about things humans take for granted.
I love the interactions of the host teaching his bots rather than just playing with them.
Like when the bots and Joel discussed death when laying in coffins.
Or when Mike and Crow were explaining what was meant by “the 50s” and “60s”.
You mean when Emperor Claudius died?
My biggest issue with the Netflix seasons was how it often felt like just three of the same guy, with very little to distinguish their personalities. Stuff like this helps a lot.
The only issue I could see with this is that we’re supposed to be in season 13. In addition, it’s been 30 years. Unless there’s something that resets the bots to their previous unfamiliarity with humanity, it really doesn’t make sense, even within the loosely defined universe of MST3K.
By season 5, Mike doesn’t do much with teaching the bots how to be human. It’s actually quite rare. That’s something that mostly ended in season 3 or 4, really.
I agree that there needs to be something that differentiates them somewhat, but I’m not sure that’s it.
This has, I think, always been a slippery matter.
In “Futurama”, Bender’s robot-ness is clearly calculated to make no sense at all. He might be naive in one aspect and cynical in the same aspect moments later. He feels pain, but only as required for comedy.
So, too, with Tom and Crow. Sometimes they can feel pain and fear and a sense of mortality. Other times, they’re completely glib on the topics.
That’s why I said it’s loosely-defined, but it’s been pretty well-established up to now that the bots don’t need lessons in humanity (including in seasons 11 and 12). They get what they want to get and ignore the rest. So to completely reset them to understanding nothing would require some kind of acknowledgment that things have changed. Heck, when they changed voices on the bots in the original run, they took a few seconds to address it.
Yeah, I’m just spitballing. I just repeat to myself “it’s just a show”.
I think they’ve already crossed this Rubicon but it might’ve been funny if the bots had been completely naive about the 15+ year gap in the show. (I think they’re already savvier than Jonah, tho’.)
I like the misconceptions, so think “Third Rock from the Sun”.
Joel was basically the bots’ father, but Mike always felt like more of a “big brother” figure.
Big brother or no-account uncle. 
Although I have to say they played up his incompetence way more in the SciFi years. In the CC years, he was well-read and, of course, too nice. 
Mike was the stepdad, never quite sure how far he could go in disciplining the other guy’s kids, and deciding to just stay as chill as possible until they realized they could trust him not to leave.
Having just watched Wizards of the Lost Kingdom, I know that this did happen in the Netflix years. Jonah explains to Tom that he can raise an army of the dead and woo fair maiden with “the magic in you.”