The real cal howard said:
To further my argument, there's also Counter and Mirror Coat to reflect anything that does hit. And Deoxys has insane defense boosts to add onto it.
So to summarize:
I am going to reply to your points in order
Pretty sure that taunt is temporary, so it's just delaying the invitable, and the immunity idol makes him immune to that since I am pretty sure that's also a status effects in Chronicles
Shadow already has a significant Ap advantage plus he can get stronger via Chaos Boost, Hero and Dark mode and taking off his inibitor rings, which btw don't drain Shadow's stamina in the games, plus Ap, Chaos Blast and Spear is enough to beat regen
Chaos Blast counters all of that with a large AoE attack, which Shadow can spam in Chaos Boost and Dark mode, plus Violet Void and Indigo Asteroid as well, plus Shadow can use his hover shoes or a extremy gear or the Ark of the Cosmos to catch him in the Air
Shadow can just break the forcefields via having a already significant Ap advantage, and Shadow can boost his Ap to counter the defence boost, also most Pokemon are vulnerable while boosting their stats, meanwhile Hero and Dark mode allow Shadow to not take any damage from Sonic's attacks, so Deoxys also won't harm him
The Dark and Hero mode natural invulnerability plus the invencinbility monitor and Wisps can counter reflected attacks so that Shadow won't take damage, also Shadow can attack him in the stopped time as well.
Also Shadow can revive himself twice thanks to his equipment, so if Deoxys beats him, Shadow will revive and imediately finish him off with a wisp or BFR in stopped time, the Wisps will work in stopped time since Rouge and Omega can still move after Shadow stops time after Team Dark's team blast, and before someone says that's game mechanincs Charmy and Vector don't follow Espio when he is invisible, so they could have done the same for that
Shadow can also heal himself via Shadow heal or many equipments as well in case Deoxys does significant damage, can inducd fear, boost his own speed, absorve his life force, or paralyse him with a Chaos Spear or Stun