Why does Fred like his new GPS despite it being generally rude and unhelpful? It acts and sounds similar to his father, Mayor Jones, from Mystery Incorporated. Going with the theory that the '10s-era movies take place in the new timeline from the end of Mystery Incorporated, Fred probably misses how his false father used to act, since Jones doesn’t suffer from Comedic Sociopathy in the new timeline. Doubles as Harsher in Hindsight, as this movie was released shortly after Mystery Incorporated began airing, so one could've safely assumed at the time that he was using his GPS as a Replacement Goldfish for his father while on the road presumably after whatever events unfolded at the end of the show.
Velma having a little sister we’ve never heard of before that attends an academy focusing on stage magic away from home can make sense in the Mystery Incorporated continuity, as we know that Angie has loose parenting and would be fine with letting her children pursue their ambitions as long as they stay out of trouble.