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Mewtwo can also use Shadow Ball, and if you wanted to use Shadow Ball effectively as Deoxys, you would need FR Deoxys, which dies easily. I'm afraid Mewtwo is better. Just look at its stat totals. I will never accept Deoxys as better because it is simply not.
At the current moment, Mewtwo would probably be the better. Deoxys LG is the one with the best chance of defeating Mewtwo with Shadowball. Deoxys RSFR will probably end up being defeated if Mewtwo is the faster. if Deoxys FR gets the speed it needs, Mewtwo will be done.
Once the Emerald Deoxys comes out, Deoxys FR will dominate. Let it learn Extremespeed in Emerald then trade it over to FR to get it's attack stats.