It's not as much a question of what Deoxys-D lost as what its environment gained. Its base 50 HP is pathetic, and simply not enough for taking on new or improved threats like Kyogre, Arceus, and Palkia. Also detracting from it as a wall is its pure Psychic typing with Pressure, which doesn't offer useful resistances. Psychic and Fighting are almost never used in Ubers, Psycho Boost Deoxys-A usually has Shadow Ball, too, and Fighting Arceus will just Toxic Deoxys-D. This brings me to the next point, which is its helplessness in the face of Toxic Spikes, which has become quite popular in Ubers. It can use Spikes and Stealth Rock, but is generally outclassed by Forretress, which can set up Toxic Spikes while it's out as well.