I still think that you are exaggerating the issue. For missions the Its fairly even between these ships.
There are some Apples to Apples comparisons. These fits are bit bling because HS missions.
Prot Vs Deimos
Tank ~700 vs ~900
DPS 802 vs 729
Speed 559ms vs 762ms
Warp 4.5au vs 3.3au
So sure, in some way the Deimos is better but in the 2 main ways for missions its not (warp speed and DPS).
[Deimos, mission]
True Sansha Medium Armor Repairer
Corpus X-Type Armor Thermal Hardener
Corpus X-Type Armor Kinetic Hardener
Shadow Serpentis Magnetic Field Stabilizer
Shadow Serpentis Magnetic Field Stabilizer
Shadow Serpentis Magnetic Field Stabilizer
Shadow Serpentis 10MN Afterburner
Thukker Large Cap Battery
Tracking Computer II, Optimal Range Script
Tracking Computer II, Tracking Speed Script
250mm Railgun II, Federation Navy Antimatter Charge M
250mm Railgun II, Federation Navy Antimatter Charge M
250mm Railgun II, Federation Navy Antimatter Charge M
250mm Railgun II, Federation Navy Antimatter Charge M
250mm Railgun II, Federation Navy Antimatter Charge M
Medium Ancillary Current Router I
Medium Hybrid Collision Accelerator II
Hobgoblin II x5
[Proteus, Test]
Shadow Serpentis Magnetic Field Stabilizer
Shadow Serpentis Magnetic Field Stabilizer
Shadow Serpentis Magnetic Field Stabilizer
True Sansha Medium Armor Repairer
Corpus X-Type Armor Thermal Hardener
Corpus X-Type Armor Kinetic Hardener
Shadow Serpentis 10MN Afterburner
Republic Fleet Large Cap Battery
Tracking Computer II, Optimal Range Script
Tracking Computer II, Tracking Speed Script
250mm Railgun II, Federation Navy Antimatter Charge M
250mm Railgun II, Federation Navy Antimatter Charge M
250mm Railgun II, Federation Navy Antimatter Charge M
250mm Railgun II, Federation Navy Antimatter Charge M
250mm Railgun II, Federation Navy Antimatter Charge M
250mm Railgun II, Federation Navy Antimatter Charge M
[Empty High slot]
Medium Auxiliary Nano Pump I
Medium Auxiliary Nano Pump I
Medium Hybrid Collision Accelerator I
Proteus Core - Augmented Fusion Reactor
Proteus Defensive - Nanobot Injector
Proteus Offensive - Hybrid Encoding Platform
Proteus Propulsion - Hyperspatial Optimization
Hobgoblin II x5