These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Fridge Horror: The aliens in 5th Grade are running the experiments to find out how many specimens to get...so they can breed all of them on their planet.
Genius Bonus: They contain loads of references to famous historical figures, scientific concepts, stories, and other things that the kids playing probably don't recognize. For example, the Goo Lagoon in 3rd Grade is full of references to famous British characters, such as The Beatles and Eliza from Pygmalion.
Narm: The voice acting in "Incredible Toy Store Adventure", since the voice actors wouldn't sound like actual children, they hired new voice actors. Let's just say... Narm and Dull Surprise abound...
Ship Tease: Some people take the interactions between Santiago/Joni and Owen/Leslie in the early games as this, particularly the latter since they seem to be engaging in G-rated Unresolved Sexual Tension. A case can also be made for Joni's interactions with Owen in later games since she seems to only get annoyed with him in Reading but that's only because he's smitten with the princess they're supposed to helping.
Technology Marches On: The kids keep in contact with each other using "videophones" invented by Santiago. At the time the games were made, commercial camera phone did not exist in North America and regular cell phones were not widely used by children anyway.