It could have been the other way around; the game was always planned to have this plot twist, and the writers of the film were aware of this and decided to incorporate it into the script of the film.
But the crew said that the ending would be different.
The ending of the first game was different in one manner. Harry chose to remain as Detective Pikachu because of two reasons revealed in the sequel. The first reason, as given by Mewtwo, was that returning Harry's consciousness to his original body would have a 50% chance of killing both Harry and Pikachu because of how intertwined the two had become over the course of the story. The second reason was that Harry wanted to see his son grow up, and he can't do that if he's dead. The twist wasn't that Harry was stuck as Pikachu. The twist was that Harry had to give up his memories and any abilities in order to save his partner and his family.
Did the film (which exists in the universe) give Tim a hint in-universe?
Probably not, since Tim and even Pikachu would initially dismiss the film's conclusion on the basis of its inaccuracies.
Why couldn’t Mike Baker and Amanda Blackstone help in the game?
Probably because all of the help they could have possibly provided in the field would have been overshadowed by the abilities of the other Pokémon that assisted. Their office was also the closest thing Tim and Pikachu had to a "hub" between chapters in the old game, and that position was mostly overtaken by Tim's apartment now that it added Tim's mom and little sister.
Tim's still in school, and the Baker Detective Agency has lots of other cases to solve. Tim would be available for very unusual Pokémon problems while Mike and Amanda handled the more usual problems.
"Photographic evidence" (SPOILERS FOR CHAPTER 3!!)
Butler claimed to have evidence of Pokémon committing crimes, but he never shows the actual photos to anyone, not even the press. As it were, all the original photos depict a Ditto with a Control Cube on its backside. How did he expect the local population to accept this "evidence" if he hasn't gone to the point of editing the pictures? Does he assume that the people of Ryme City are gullible morons?
To be fair, the only photo we actually see is the one of Ditto-as-Pikachu. While that one is pretty obvious, it could be that the Control Cubes are better hidden in the others.
