Other Options

Leftovers is an alternative if running Spikes in conjunction with Cyclizar, simultaneously lessening pressure to constantly use Recover and making it easier to set multiple layers of Spikes. Rocky Helmet punishes Maushold and prevents Jirachi from trying to flinch Deoxys-D until it gets KOed. Tera Steel gives it a Flying and Bug resistance and much more valuable defensive typing, though it makes it weaker to wallbreakers like Mamoswine. Future Sight could be used to force switches with Teleport to maneuver into an advantageous situation, but it is often too weak. Night Shade gives Deoxys-D consistent, if middling, damage. Mental Herb can negate Taunt from the likes of Krookodile and Noivern once, but other items are more consistent. Deoxys-D can sweep with a moveset of Cosmic Power / Stored Power / Recover / Night Shade, but it often gets overwhelmed and hates the prevalence of Dark-types.

Checks and Counters

Dark-types: Dark-types like Bisharp, Krookodile, and Crawdaunt can switch into anything Deoxys-D can throw at them and set up or threaten it out with super effective STAB attacks. However, they usually don't appreciate Knock Off, and some cannot break through Deoxys-D if it's running Colbur Berry.

Setup Sweepers: Slow setup sweepers like Reuniclus and Registeel can use Deoxys-D as setup fodder unless it's running Taunt. Similarly, non-Thunder Wave variants will let faster sweepers like Armarouge and Gyarados set up with impunity.

Ghost-types*: Gengar can potentially set up against or irreparably damage Deoxys-D. Basculegion-F and Golurk can switch into Deoxys-D and threaten it out easily; Golurk can even block its Thunder Wave. None of these Pokemon like to take a Knock Off, though, and Gengar and Basculegion-F must be wary of paralysis.

Chip Damage: Entry hazards can wear down Deoxys-D easily throughout the match, forcing it to waste turns using Recover. Deoxys-D has a tendency to lose its item because it's often a switch-in to Pokemon like Galarian Zapdos and Mamoswine, and this can make entry hazards problematic. Similarly, although Deoxys-D checks Pokemon like Galarian Zapdos, Jirachi, and Barraskewda, if they click U-turn or Flip Turn, it will cause a lot of chip damage, which can compromise Deoxys-D's ability to pivot effectively.