Mewtwo:
HP: 106
ATK: 110
DEF: 90
SPA: 154
SPD: 90
SPE: 130
Generally, Mewtwo should be more stable that Deoxys. This is probably one of the strongest movesets for Mewtwo:
Mewtwo w/ Brightpowder
Ice Beam
Thunderbolt
Calm Mind
Recover
With this, Mewtwo can boost Ice Beam and Thunderbolt to dangerous levels. The only monsters that resist this moveset are Chinchou, Lanturn, and Shedinja. Of course, Mewtwo is not invincible; Slaking can probably OHKO it with Choice Band, Hyper Beam, and the right stat distributions.
Deoxys (NRM / ATK / DEF / SPE):
HP: 50 / 50 / 50 / 50
ATK: 150 / 180 / 70 / 95
DEF: 50 / 20 / 160 / 90
SPA: 150 / 180 / 70 / 95
SPD: 50 / 20 / 160 / 90
SPE: 150 / 150 / 90 / 180
Deoxys has many forms. Attack form boasts attack power that is greater than Mewtwo, but it has virtually no defenses whatsoever. Defense form is hard to compare, because it relies on a different strategy. Speed form doesn't have much attack power behind it and it is probably better to go off with the Speed form than the Normal form, since the Normal form probably can't survive a hit, either. Attack form cannot pick up Recover (it MIGHT be able to if you trade Deoxys from Ruby / Saphire to FireRed. Still, its attack stats are high enough to where it can probably OHKO many monsters without too much trouble, leaving the other slots for other moves. If it gets a Calm Mind or two behind it, virtually nothing will stop it. Psycho Boost will probably KO many monsters that have low HP and / or a low Special Defense. It can also pick up Superpower, if you want a Physical attacker.
I think this is very close. I like Deoxys because of its high speed and the potential to sweep an entire team if I manage to get away with a Calm Mind or two. However, Mewtwo is more stable, and can continue to fight back if a strong opponent hits the field.
Deoxys is more risky, but more powerful. Mewtwo is well-rounded. Take your pick.
Oh yeah, if Mewtwo and Deoxys were to fight each other, Mewtwo would win because of Deoxys' poor defenses.
I don't use the top tier legendaries in competitive play because they are unbalanced. Deoxys technically isn't a top tier legendary (it has the same base stat totals as Mew), but I consider it to have the power of one.