• Zen Headbutt hits Gengar and Giratina-O harder than Charge Beam, but Charge Beam will hit Tyranitar and the rest of the Dark-type squad harder than Zen Headbutt.
• If you're using primarily Tyranitar, other Dark-types, or Shadow Ball Mewtwo, Thunderbolt will be the hardest-hitting Charge Move to go against.
• If you're using primarily Gengar and Giratina-O, Psycho Boost will hit the hardest. Gengar in particular will benefit greatly from dodging Psycho Boost.
• Hyper Beam has high base power, but it comes out less frequently than the other two Charge Moves, is easier to dodge, and hits Gengar and Giratina for minimal damage.

• Fog boosts the power of your Dark- and Ghost-type attackers; unfortunately, Fog in-game is extremely rare.
• Wind boosts the power of Deoxys' Psychic-type attacks. If you can't dodge consistently, Gengar's performance will suffer greatly against Windy-boosted Psycho Boost sets.
• Rain boosts the power of Deoxys' Electric-type attacks, as well as the power of your own Bug-type attackers.

Ghost-types tend to perform better against Hyper Beam due to their Immunity-tier resistance against Normal.

Dark-types are naturally stronger against Psycho Boost due to their Immunity-tier resistance to Psychic.

Gengar is not listed because you must be able to dodge consistently. If you are able to consistently dodge Psycho Boosts, Gengar is by far the best counter.

Thunderbolt is the hardest Deoxys moveset to go against, but the overall difficulty of the fight is still very low - Level 20 Giratinas can consistently duo 100% of the time, even against Thunderbolt.