Detective Pikachu did a very good job of not being 100% Kanto fanservice, which it easily could have been. I was too busy being pleasantly surprised by the representation across multiple generations to think of Pokemon who were left out.
I suppose the obvious place to start would be (no pun intended) some of the starter Pokemon. Torterra and Greninja both had major roles in the movie, but Infernape, Empoleon, Chesnaught, and Delphox were nowhere to be seen. That would have been nice.
The other main place I can think of is the flocks of bird Pokemon. From what I recall it was pretty much nothing but Pidgey, Pidgeotto, and Pidgeot. It shouldn't have been too much hassle to include common bird Pokemon from other regions.