If we go by the games, it's the same scenario. Mewtwo uses his ridiculous speed and sp. attack stats to attack first and either kill Ness in one hit or disable him and then finish him off afterward.
Incidentally, his ability is Pressure, which makes PP usage double for all of his opponent's attacks.
It's impossible to ORKO Ness due to his rolling hp meter. Also any damage done to Ness is reflected back to Mewtwo unless his abilities fall under PSI energy. A Ness who abuses the rock candy glitch has 255 in all of his stats and 999 hp and pp. Without abusing that glitch and simply through rng abuse Ness at level 99 has the stats of:
HP: 924
PP: 666 (loldevilwut)
Offense: 179 (+100) = 279 [ingame this counts the same as 255 though]
Defense: 51 (+80) (+30) (+80) = 221
Speed: 62
Guts: 85 (+127) = 212
Vitality: 61
IQ: 86
Luck: 81 (+30) (+35) = 146 [see notes]
Numbers in parentheses are stat boosts from equipment. Numbers in {} are from stat boosting capsules found throughout the game.
Equipment:
Gutsy Bat
Goddess Band
Star Pendant
Souvenir Coin
Resistance to sleep, fire, freeze [ice], flash, and paralysis.
*Offense and Defense deal with non psi moves. IQ is the same as the special stat in red and blue. When Ness uses his offensive move, he has a 1/16 chance of missing. I cannot find the guide that lists all the details on how critical hits and his evasion is calculated though...
Notes: HP and PP cap at 999. All other stats cap at 255 (even if his equipment would raise it past that number, it would still act the same as being at 255). With the way the game calculates Luck, it is worthless to increase it past 80.
Also, if we allow Ness to use items then he becomes practically invincible. Kraken soup fully heals his hp. Brain Food Lunch heals 300 hp and 50 pp by itself and combined with a jar of delisauce fully heals hp and a large amount of pp (dunno the exact amount of pp). There is also the magic truffle whcih heals 80 pp and is also boosted by the jar of delisauce (forgot the amount it's boosted). He can carry several of these.
Abilities:
Psi teleport gives him the ability to teleport (duh), run really fast, and
stop time. There is also an alternate version where he spins around wierdly. Cost: 2/8 (the spinny version is the more expensive one)
Psi lifeup he can fully restore his hp. Cost: 13
Psi Healing can heal any status affect that afflicts Ness. Cost: 5, 8, 20, 38 (depends on the status effect)
Psi powershield halves all non psi damage taken and reflects the other half back to the opponent. Cost: 10
Psi Paralysis and Pk Flash give him a wide variety of status effects he can afflict his enemies with (PK flash gives a chance for an instant KO) Cost: 8-32
Lastly Psi Rockin can deal up to 960 damage. It has a chance to miss, but I can't find the equation for that right now... Cost: 96
Now let's look at Mewtwo:
Max Stats:
HP: 416
Attack: 350
Defense: 306
SP. Attack: 447
SP. Defense: 306
Speed: 394
If we look at the strongest move he can learn [hyper beam, yea I know this move sucks, I just looked through his move list and picked the one with the highest possible power] and I'll assume it uses his SP. Attack stat (I have no clue if how moves are calculated in pokemon). I'll just use the equation attk power of move + sp. attack = damage dealt to Ness since I'm too lazy to factor in his defence. We see that 447 + 150 is 597 total attack power. Even if it had the power to ignore Ness's defences (which it doesn't) it is not powerful enough to deal 924 damage. It also should be noted that even if Mewtwo was able to deal that much damage to Ness, Ness hp is a rolling hp meter (look a video of a battle in earthbound if you don't understand) meaning that he would have enough time to heal himself.
Why did I take the time to post this? I dunno, I'm bored lol. I'm not done with this yet, but I really have to go to sleep now.
TL;DR version: Ness has a rolling hp counter, the ability to stop time, heal himself, and powershield himself. How does that not beat everybody besides maybe Lucas?