A lot of the science is updated in this new show, which makes sense; the original cartoon was over 20 years old. So some of the science could have been re-examined since the original viewers were children, so it helps to reevaluate it. So older fans can have something to look into; the new updated look in the science department.
When the class goes atomic-sized in "The Magnetic Mambo" and "Three In One", they are all wearing helmets that have a screen over their face. Which makes sense, much like when it was the original cartoon. One may not always think about it, but there's no breathable air at that small of a scale, so if they were gonna shrink that small, they'd need something to allow for them to breathe.
The train sets Wanda's little brother is shown playing with look exactly like BRIO - which use magnets.
Why do they have to persuade the principal to allow a pet rat, but not Liz? He's allergic to animals. And this is a very good reason as to why the kids say he has to be persuaded - some schools don't allow pets with fur for this very reason!
Arnold states in "In the Swim" that he hates winter and the cold. Might that have something to do with his past experience on Pluto?
Janet's behaviour is much, well, nicer this time around. Well, the kids are older - Janet simply matured.
Phoebe going back to her own school could be the result of her parents finding out about Miss Frizzle's daily field trips and not approving.
Jossed because Phoebe's Dad was in the original Magic School Bus series with other parents (and in one case grandmother) when Ms. Frizzle takes the parents on a trip in "Going Batty" (albeit a fairly tame one for the Friz). He even says he's glad he transferred her from the other school.
However, we only see Phoebe's dad. Where's her Missing Mom? Maybe this Fridge Horror is because she didn't like it.
