I wouldn't call Lucario a replacement for Mewtwo. Clearly they were both planned for the game. Due to time constraints or what have you, they decided that they could only give Pokemon so many representatives. Cutting Pikachu would be ludicrous, for obvious reasons. Jiggs is just as much a veteran to the game as Pikachu-- that is to say he's pretty iconic to Smash at this point. Pokemon Trainer was an entirely new type of character, and a similar concept was planned for melee (I think this is true, apologies if that's incorrect) so it wouldn't quite make sense to cut him. So the choice of cuts would be between Mewtwo and Lucario. Tough choice, considering they fill very similar niches in the Pokemon universe (They're both legendary/pseudo legendary, both capable of thought/speech, both stars of a movie). Now Mewtwo has the benefit of being a Smash veteran, but Lucario has the benefit of being more relevant. Also, for what it's worth, Lucario has the benefit of being a new face, and newcomers are always fun. It would make sense to cut Mewtwo instead of Lucario.
tl;dr Lucario is not a replacement for Mewtwo. More of an 'update.'
All that said, I'd love to see Lucario get the boot so Mewtwo can come back.