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.
Backup dancers are super-strong robot versions of the leads, built by the bongo player(s).
Family-Unfriendly Aesop: While the titular duo are messiahs who usher in a peaceful utopia with their music, they get to that point by using time travel to manipulate their lives for the better, making this a benign but still prevalent case of Utopia Justifies the Means.
When Freud is coming on to some girls, he tells them that they "seem to be suffering from a mild form of hysteria."
The references to The Seventh Seal.
The guys spotting some weakness in Napoleon's plan for the Battle of Waterloo. Made funnier because their tone implies they're not using historical knowledge; two idiots just noticed a flaw that the emperor didn't.
When they pick up Joan of Arc, Ted briefly mimics the well-known picture of God and Adam from the Sistine Chapel.
Genghis Khan is shown forcefully making out with a servant girl - why do you think he supposedly has descendants across half of Asia?
Hilarious in Hindsight: How ironic that Jim Martin of Faith No More, "founder of the Faith No More Spiritual and Theological Center", quit Faith No More only two years after his appearance in Bogus Journey.
William Sadler plays Death in the second film and performs a Heel-Face Turn when Bill and Ted defeat him. A few years later in Demon Knight, he plays The Chosen One that battles the forces of Hell to stop them from conquering the universe.
It Was His Sled: The fact that Rufus's future is based on Wyld Stallyn's music is a bit of a Reveal at the end of Excellent Adventure, but anyone explaining the plot mentions it right away.
Not exactly - Rufus does mention in the opening blurb that it's thanks to Bill and Ted's music that the future is what it is, and that it very nearly wasn't the case. The film further emphasises the importance of Wyld Stallyns when they accidentally visit the future and get another hint of their importance.
Values Dissonance: When Bill and Ted hug, they always push each other away and humorously shout "Fag". This was okay for an 80's movie that was rated PG. That term is less acceptable now.
The same goes for the sequel, where the guys attempt to talk the Evil Robot Usses out of killing them by saying "We love you!", prompting the ERUs to say "Fags!" and then kill them anyway. Though that might have slipped under the radar because it kind of sounds like a sarcastic "Thanks!"
The sequel might actually be hanging a lampshade on the word not being acceptable to use. After all the ones using it are the evil Bill and Ted, who are overall more immature and mean than the real thing. The real Bill and Ted hug in the sequel without a real problem, indicating they've grown up a bit.
What Do You Mean, It's for Kids?: Take a lighthearted, family-friendly Totally Radical comedy and add lots of terror along with a Played for Laughs—yet still effectively morbid—Disney Death plotline, heavily ramped up profanity, sexual dialogue and incest references, and quite a few instances of Ho Yay as well, and you've got something that probably didn't sit nearly as well with the original film's target audience.