Four characters per franchise. It's as simple as this. Lucario didn't replace Mewtwo, but Mewtwo didn't fit at the roster when the more popular and current at the time Lucario was added. You could as well say that Red replaced him, but would that be true? Pokémon Trainer was a unique feature character, while Lucario was essentially Mewtwo's successor as the cool, fighter-esque Pokémon smasher.
Whether or not Lucario will return depends on how big a roster Sakurai wants to make. We do know Sakurai doesn't like cuts and he will hopefully add an additional position for each franchise -- but as it stands, Lucario is the weakest link of the Pokémon roster and the most likely to be replaced.
