Passiveness doesn't really work in doubles. If someone's being passive, their teammate is probably getting a 2v1.
Not to mention, Ness/Villager/G&W being the most popular doubles characters doesn't make the best environment for using Shadow Ball offensively.
Evasion and passiveness also require space, which you have less of in doubles.
I play a lot of doubles myself (my brother and I are the top ranked doubles team in WI), and although it's unfair to compare Mewtwo to Link (who is a great doubles partner), I definitely feel much more hindered in teams now that I've switched mains; I also feel more hindered than in singles with Mewtwo.
I partner with the #1 Ness on Anther's Ladder, and we do extremely well. It takes a very different mindset. At first, I told Shamrock that it couldn't work. Too much pressure and chaos, etc. Shamrock taught me a different style of play, though, and it works.
At locals, I have finished many doubles matches with all 3 stocks because of the playstyle. It doesn't put significantly extra pressure on your partner when done right, because you are maintaining pressure with Shadow Ball from afar.
Think of it this way:
Every Mewtwo player agrees that Mewtwo is a strong defensive character. The problem comes when the opponent is defensive, and Mewtwo has to go on the offense. He just isn't good in that scenario.
In doubles, the opposing team either has to be extremely aggressive against Mewtwo, which Mewtwo can counter, or they go after his partner out of frustration. These are both wins for him.
I am not saying he is the best doubles character ever, but it is strong. I will try to upload some matches at some point to illustrate the concept.