Yeah, Mewtwo was replaced with Lucario. As much as I hate this as you do, there are a number of reasons:
1. Mewtwo was very off balanced. In other words his statistics did not match. He had excellant attack power but was very weak to close-up attacks.
2. Lucario is the latest representative of the Pokemon Games (aside from Pikachu and Jigglypuff) considering Diamond and Pearl are the latest versions out.
3. Lucario might be a different type to Mewtwo (I'm not too familiar with the Sinnoh pokemon, only from Kanto-Hoenn, including Johto) because Mewtwo is a Psychic and Lucario is a Fighting/Steel type. However, Lucario has the power of Aura which most of his attacks revolve around. And a number of his attacks are similiar to Mewtwo's as well.
Now imagine if let's say we put these two into Brawl, they'd look too identical to one another considering they are both humanoid in appearance. People who aren't too familiar with Pokemon will think they are clones of each othere and in a way, that is necessarily the case here.
Though it is tragic for Mewtwo to be leaving the series along with Roy, they have been replaced for the better I might say. Although Mewtwo would've been great as a villain in the Subspace Embissary (there are also Bowser and Ganon who are also on the evil side along with Master and Crazy Hand but there is more to it, there is an even darker force behind everything).
The pokemon characters have always been my favourite overall. I guess adapting to Lucario will not be so bad. Plus his attacks are much more accurate and just as strong (remember Mewtwo's shadow ball was very hard to get an accurate shot with, Lucario's Aura Blast is much more accurate, and can also perform well at close range too).
I reckon Pokemon Trainer is gonna be awesome, especially now that we finally get to use CHARIZARD!!!!

The one that we had to summon from Poke-Balls in the first and second games, is finally controllable. That is so awesome!
My only hope is that they make a 4th game.