you know if mewtwo is considered a bad guy, then thats probably the main reason why he didn't show up with the others. So far in the adventure mode the only characters shown playable were the good guys right? And I imagine that the Sub Space Emissary is only playable with the good guys.
You know what my logic may not stand since I just noticed a picture on the Dojo that has stickers usable for Kirby, Metaknight, and Dedede. Now I do consider them bad guys but we all know they are "good" sometimes. So maybe they are with the good guys as well? Hmm... but the leaders of what ever those new things are called do have Metaknights ship, so did they steal it or did he loan it out? Those 2 are in a very gray area.