They're both awesome. This is probably how the battle could go...
Deoxys, being in atk form, uses shadowball. However, Mewtwo dodges it, and attacks with darkpulse. But, Deoxys uses thunder to neutralize it. Switching to Defense Form, Deoxys uses spikes, covering the battlefield. Mewtwo begins levitating, and uses darkpulse. The attack sends the less nimble defense form deoxys back aways. Mewtwo tries a shadowball, and just when it looks like it is going to hit, Deoxys uses Mirror Coat, bouncing the attack back. Mewtwo enragedly surrounds its body with energy befor using Psystrike. Deoxys switches to attack form, and hurls a Psycho boost. Both attacks collide, and both 'mons are knocked out!
You're pitting my favorite Pokemon against possibly my least favorite Pokemon- which should I choose:banghead:? MEWTWO!:banana:!!!!!!!!!!!! It's awesome, cute, and relatable. Deoxys' a fricking creepy alien. I don't dislike it that much, but MEWTWO IS SO MUCH BETTER!:saiyan:!!!!!!!!!!!! That's all....
Mewtwo is my favorite Pokemon overall, so I easily vote for it. Since I consider it to be the most powerful Pokemon in existance, I of course would find it more useful in battle. It's among the best Pokemon in terms of Special Attack and Speed, and it has more HP than Deoxys in all of its forms. To cap it off, it has higher defenses than at least two of the forms of Deoxys, so Mewtwo doesn't faint as easily when it gets hit. I could keep going on, but I feel I must stop.
I voted for both.
While I prefer Deoxys' concept and design, Mewtwo is nothing but an awesome-looking legendary.
I referred to my friend the damage calculator and an average Deoxys-A with a Life Orb can't OHKO an average Mewtwo with a Shadow Ball, but an average Mewtwo can OHKO Deoxys-A with most neutral attacks, plus Mewtwo can actually take a hit so I voted Mewtwo
Mewtwo, I never liked Deoxy's designs. Plus Mewtwo looks like a mutated cat, and I love cats.