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Mewtwo is harder solely for the fact he is level 70 while Deoxys is only level 30. Mewtwo also has safeguard and recover, which can thwart your catching strategy easily.

If you want to judge for yourself:

Deoxys Lv. 30 Mewtwo level 70

Knock off (DRK) Swift (NRM)

Spikes (GRD) Psychic (PSY)

Psychic (PSY) Safeguard (NRM)

Snatch (DRK) Recover (NRM)

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