I hear this question alot, and the honest answer is that nobody but Niantic knows.
However, I very much doubt they would permanently cut off access to any pokemon. Perhaps variations, like the Pikachu with hats, but not the basic versions. I expect all the legendaries will still be in the game, but likely less common than they are now. May still be in raids as a rare occurrence, and may even be catchable in the wild or in eggs.