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Just wondering

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Deoxys learns way more special moves than physical moves
Special Deoxys.
The majority/best of its moves are special attacking
How do you know which moves are the best?
Deoxys is a really bad choice for NatDex AG. It's outclassed by Calyrex-S, the premium Psychic-type in the tier. If you anyways want to run Deoxys, a mixed set is best for it. Superpower + Psycho Boost can punch through most bulky balances and offences, especially if running Focus Sash but is usually downed by Marshadow and/or Arceus long-term.
By Deoxys, which form are you referring to?

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Deoxys isn't a good choice for NatDex AG. As an offensive Psychic-type, Calyrex-Shadow outclasses it. As a wallbreaker, though, almost anything with expansive moves and good offensive stats can work in NatDex AG. Deoxys-A has a small niche as a one-time gamble, which can work well on offences.
Also, please keep in mind that I'll be answering this for Deoxys-Attack. The only other viable Deoxys forme, Deoxys-Speed, doesn't work as an offensive Pokémon, and other forms are not viable in the tier.

Overall, Mixed Deoxys-A is the way to go in NatDex AG

  • Deoxys-Attack, by its good speed tier and offensive stats, can punch holes in most bulky offences and balances alike. It can muscle past most defensive Arceus formes and the defensive backbones of the tier; Eternatus, Necrozma-DM, Arceus-Dark and Yveltal. On the switch-in, it can 2HKO most walls and tanks with its expansive coverage as well as 180 base offences.

  • Item: It can choose its items between Focus Sash and Life Orb, depending on what the team appreciates more. Life Orb has the perk of getting a few OHKOs that non-LO can't touch. Also, as Deoxys-A is very frail anyways, it doesn't mind the recoil that Life Orb inflicts. Focus Sash is a choice for more conservative players. It's a one-time life saver which can help Deoxys-A to potentially get important 2HKOs on foes such as Zacian-C, Xerneas, Yveltal etc.

  • Offensive Moves: Deoxys-A can't work solely as a special or physical sweeper, it wouldn't get its required coverage. Physically, you're usually using only two moves, Superpower and Pursuit. Superpower hits Dark-types such as Arceus-Dark for super-effective damage, letting it get past its supposed-to-be check easily. Low Kick is also another viable option; it's not supposed to hit light targets such as Klefki and Magearna here. Pursuit lets Deoxys-A trap Ultra Necrozma, non-max speed Calyrex-S, Mega Gengar etc; which it naturally forces out. Psycho Boost is a mandatory STAB; dealing massive damage to most Pokemon that don't resist it. As the fourth move, you're free to run anything by your build.

  • Support Moves: Both of Deoxys-A's preferable items work well with Spikes, which is a good option to take advantage of the many switches Deoxys-A forces. With most opponents constantly pivoting between their Yen core, they'll find themselves under substantial pressure from Spikes later in the match. It also forces Yveltal into mind games over whether or not it should use Sucker Punch. Stealth Rock is another option, but as Rock-weak Pokémon are good switch-ins to Deoxys-A, it's not worth using than Spikes.

A standard offensive set for Deoxys-A looks like the following:

Deoxys-Attack @ Life Orb / Focus Sash
Ability: Pressure
EVs: 4 Atk / 252 SpA / 252 Spe
Naive Nature
- Psycho Boost
- Ice Beam / Extreme Speed
- Low Kick
- Pursuit

Other options

  • Deoxys-A can also be used as a lead. It can fake offensive sets easily, and with its ability to force constant switches, getting hazards up would be fairly easy. It also has coverage to ward off most Defog users and can put considerable pressure on most bulky builds. It can also be used as a last resort to punch holes in the opposing team late-game.

  • Nasty Plot Deoxys-A is another viable set. With Nasty Plot + Focus Sash, you're usually guaranteed one turn of set-up, and after a +2 it can decimate most defensive walls with ease. This set is thoroughly outclassed by Calyrex-Shadow, though, which can do what Nasty Plot Deoxys-A does but better. This set is still a good lure and can come useful in some niche cases.

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In what situations is attack Deoxys outclassed by neither speed Deoxys nor Calyrex?
Deoxys-A is a bad Pokémon for NatDex AG. You'll usually not want to use it. Deoxys-S has a niche as a hazard setter, one of the best for offensive teams in the metagame. Deoxys-A is not outright outclassed by Deoxys-S; the latter is always used as a lead. Both fulfil different roles with their orthodox sets.
Calyrex-S usually requires less conditioning and is not a one-time play. I'll still maintain that there is no apparent reason to use Deoxys-A than Calyrex. But you're free to run a lot of niche things which can work as lures in NDAG.
Fwiw Deoxys-A doesn't require a Z-Move to break through Arceus-Dark, which leaves the Z slot free for Necrozma, Eternatus or Arceus.