The discussion on whether the game is more balanced with or without customs is already happening on facebook. Its probably time to have that discussion here as well. Two primary arguments:
1) The game and its balance patches arent balanced (or minimally balanced) around customs, as seems to be the case on the latest update
2) There seems to be no desire to partially ban certain customs, so given the choice between all customs and no customs those in favor of partial bans prefer no customs
We're also having a discussion on this in the "Competitive Smash Ruleset Discussion" if anyone else wants to participate. I feel it's a better fit for that thread than this one.
Anyway, on to my thoughts about M2. I played a lot of him last night. First of all, dude hits HARD. His USmash is almost comically powerful, consistently killing around 90%, god forbid if he has significant rage. I killed a Peach at like 70% last night when I was at 150%. UThrow, FSmash, DSmash, Fair, Shadow Ball, and all also solid kill options. His punish game is almost Ganondorf status. Do not airdodge carelessly against this guy or you will pay.
Mewtwo's neutral game is also generally decent. He has decent pokes, his throw is terrifying, he has a solid command grab / reflector, and Shadow Ball murders shields so it can force approaches. His Jab 1 is a very scary attack, as those jab cancels are hellishly legit. Jab into grab is legitimate murder considering the potency of his throws.
Where Mewtwo falters is that his defense is completely awful, maybe the worst in the game. Besides being big and light, he also has utterly godawful OOS options, with Nair and Grab being the only two viable ones and they're both slow. His one saving grace is that Teleport is a fantastic move in disadvantage, but with M2's weight you really can't afford to be put into disadvantage all that often in the first place. I feel like he is forced to rely on spotdodge very heavily, as he has great punishes after a successful spotdodge, but you'd better have good reads or you're going to get rekt.
Matchup-wise, his matchups against fast, annoying characters like Pika and Fox seem completely terrible. He just doesn't seem to have any good answers to their pressure that doesn't involve taking big risks, and they're rarely susceptible to big punishes. He can put on the damage if he gets his momentum going, but generally winning the damage race seems very hard. Matchups against more average speed characters and zoners seem okay, confusion shuts down a lot of zoning and he can slug it out with most characters due to his high damage output and kill power.
Overall I suspect he's likely mid or upper mid. Players with very good reads could be terrifying with him, much like Ganondorf. Actually, I feel that in a lot of ways he's basically like a floatier Ganon who trades survivability for a projectile.