This is a list of the commanders which currently have new/different abilities in my mod. (Due to modding limitations, it's not possible to see these changes until you have selected one of the affected commanders.)


GENERAL

+ Off-map howitzer barrages area of effect and damage changed to match those of similar-caliber on-map howitzer barrages (cost and/or recharge and/or shots fired changed to compensate)
+ All call-in tanks require an associated tech upgrade or structure
+ Most heavy tank call-in limits increased to two (except for the rarest ones IRL)


SOVIET

Advanced Warfare Tactics
+ T-34/85 Medium Tank replaced with IS-2 Heavy Tank

Anti-Infantry Tactics
+ Shock Troops replaced with DShK

Armored Assault Tactics
+ T-34/85 Medium Tank is a call-in instead of being buildable

Conscripts Support Tactics
+ KV-1 Heavy Tank replaced with Hit the Dirt!
+ Incendiary Artillery Barrage replaced with PTRS Package

Counterattack Tactics
+ KV-1 replaced with T-34/85

Defensive Tactics
+ Tank traps and wire fields are now one passive ability
+ M-42 AT Gun replaced with AT Gun Ambush Tactics
+ PMD-6 anti-personnel mines are now always buildable by Combat Engineers, so this commander gets a new ability, Katyusha Overwatch, based on the unused ability Scorched Earth Policy

Guard Motor Coordination Tactics
+ T-34/85 Medium Tank is a call-in instead of being buildable

Guard Rifle Combined Arms Tactics
+ KV-1 Heavy Tank replaced with Hit the Dirt!

Lend Lease Tactics
+ DShK replaced with M2HB
+ Conscript Repair Kit replaced with Repair Station
+ M5 Halftrack Assault is now M3 Scout Car Assault - the Guards squad now also comes with two Bazookas (I changed it to the scout car so the increased cost wouldn't be too prohibitive, plus in my mod the M3A1 is faster and not quite as wimpy)

NKVD Rifle Disruption Tactics
+ Recon Overflight replaced with Commissar Squad
+ IL-2 Sturmovik Attacks replaced with Tactical IL-2 Sturmovik Attack

Soviet Industry Tactics
+ Soviet Industry ability restored
+ KV-8 replaced with KV-1

Soviet Reserve Army **
+ Partisan Tank Hunters replaced with Irregulars (which can now upgrade with either 2x DP-28 or 2x PTRS instead of coming with a random LMG)
+ Assault Package replaced with KV-1 Heavy Tank
+ ML-20 Howitzer replaced with B-4 Howitzer

Soviet Shock Army **
+ ML-20 Howitzer replaced with T-34/85 Medium Tank

Tank Hunter Tactics *
+ PMD-6M Light Anti-Vehicle Mines replaced with Armored Vehicle Detection
+ Tank Hunter Ambush Tactics replaced with RPG-40 Anti-Tank Grenade Assault
+ ML-20 Howitzer replaced with Engineer Salvage Kits

Urban Defense Tactics *
+ M-42 45mm AT Gun replace with For Mother Russia!


OSTHEER

Assault Support Doctrine
+ Artillery Field Officer replaced with Assault Grenadiers
+ Tiger I replaced with leFH 18 Artillery

Close Air Support Doctrine
+ Redistribute Resources ability restored

Defensive Doctrine
+ Tank traps are now always buildable by Pioneers, so this commander gets an ability borrowed from CoH1: Advanced Warning
+ Covered Trench combined with Concrete Bunker in new Defensive Fortifications ability

Elite Troops Doctrine *
+ Troop Training ability restored
+ Tiger Ace has a fuel cost instead of income penalties

Fortified Armor Doctrine
+ Recon Overflight replaced with Riegel 43 mine
+ Elefant replaced with Tiger I

Jaeger Infantry Doctrine
+ Jaeger Infantry Command Squad replaced with Sprint

Luftwaffe Supply Doctrine
+ Stuka Bombing Strike replaced with Stuka Close Air Support

Osttruppen Doctrine
+ Supply Drop replaced with Cargo Truck
+ Covered Trench combined with Concrete Bunker in new Defensive Fortifications ability

Storm Doctrine
+ Riegel 43 mine replaced with Incendiary Mortar Shells
+ Tactical Movement replaced with Stormtroopers
+ Stuka Bombing Strike replaced with Incendiary Bombing Run
+ leFH 18 Artillery replaced with Elefant

Blitzkrieg Doctrine **
+ Command Tank replaced with Breakthrough
+ Stuka Close Air Support replaced with Stuka Bombing Strike

German Infantry Doctrine **
+ Tactical Movement replaced with Stun Grenades
+ Light Artillery Barrage replaced with leFH 18 Artillery

German Mechanized Doctrine **
+ leFH 18 Artillery replaced with Forward Supply Station


USF

Airborne Company
+ HMG and ATG drops combined into one ability: Paradrop Support Weapons
+ P-47 Rocket Strafe penetration increased and AoE profile improved
+ P-47 Strafing Run added

Armor Company
+ Elite Vehicle Crews now increases crew squad survivability
+ Assault Engineers no longer require a command point

Heavy Cavalry Company
+ Riflemen Defensive Structures replaced with Time on Target Artillery Barrage
+ Rangers replaced with Cavalry Riflemen (a four-man squad with Grease Guns)

Infantry Company
+ M21 Mortar Half-track replaced with M1 Mortar Team
+ Time on Target Artillery Barrage replaced with Defensive Training

Mechanized Company
+ Raid Tactics is now a passive ability which applies only to light vehicles
+ M21 Mortar Half-track replaced with Withdraw and Refit
+ Armor Reserves replaced with 155mm Artillery Barrage (vehicle criticals removed)

Recon Support Company
+ Raid Tactics replaced with Forward Observers
+ M83 Cluster Mines replaced with Recon Sweep
+ 57mm anti-tank gun removed from Airdropped Combat Group to allow a reduction in manpower cost

Rifle Company
+ M2 Flamethrowers replaced with Elite Riflemen Training
+ M4 "Easy Eight" Sherman is a call-in unit at 10 CP

Tactical Support Company
+ M1919A6 Light Machine Gun replaced with M21 Mortar Half-track
+ M5 Half-track replaced with Rangers
+ P-47 Strafing Run replaced with M83 Cluster Bombs


OKW

Battlefield Reconnaissance Doctrine
+ Early Warning replaced with Jäger Light Recon Squad
+ For The Fatherland! replaced with Artillery Flares
+ Goliath replaced with leFH 18 Artillery (with veteran crew)
+ Sector Assult replaced with Zeroing Artillery

Elite Armored Doctrine
+ Panzer Commander additionally increases veterency gain
+ Sturmtiger replaced with Panther Command Tank

Feuersturm Doctrine * (I cringe every time I see the name)
+ Flammenwerfer 35 is now a non-doctrinal upgrade for Sturmpioneers; this commander now replaces Volks' standard potato masher grenade with the incendiary version
+ Opel Blitz Reinforce Truck replaced with Recoup Losses
+ Incendiary Munitions replaced with Munitions Blitz

Fortifications Doctrine
+ Zeroing Artillery replaced with For The Fatherland!
+ For The Fatherland! no longer increases infantry movement speed but now provides offensive bonuses (in addition to the existing defensive bonus)

Luftwaffe Ground Forces Doctrine
+ Reconnaissance Overflight replaced with Flakpanzer IV Ostwind
+ Airborne Assault replaced with Sector Assault

Scavenge Doctrine
+ Thorough Salvage also allows converted sWS half-tracks to lockdown to gain more resources from a territory sector
+ Flakpanzer IV Ostwind replaced with Jäger Volks Upgrade
+ 105mm Howitzer Barrage fires fewer shells by default, but can fire more bonus shells than before

Special Operations Doctrine
+ Artillery Flares replaced with Goliath
+ Radio Silence is now Radio Silent Assault (infantry also move more quickly)
+ Panther Command Tank replaced with Sturmtiger


BRITISH

Commando Regiment
+ Mortar Cover replaced with an ability borrowed from CoH1: Ultra Decryption

Mobile Assault Regiment
+ M2 Flamethrower replaced with Recon Sweep
+ Vehicle Crew Repairs replaced with Mortar Cover

Royal Artillery Regiment
+ Concentration Barrage can be called in the FoW, but with very high scatter
+ Concentration Barrage now always includes airburst shells

Royal Engineer Regiment
+ M2 Flamethrower replaced with Stand Fast
+ Designate Command Vehicle debuffs (speed, RoF, etc.) reduced and separate vehicle bonuses added to the command aura
+ Vehicle Crew Repair changed to a targeted ability which works on a single, damaged vehicle
+ Anti-Building Flame Mortar Support replaced with Flame Mortar Support (works more like Incendiary Artillery Barrage)

Special Weapons Regiment
+ Concentrated Fire Operation has been restored to its original (pre-release) design: all available 25-pounders, mortar emplacements and Bofors emplacements will fire on the target location
+ Churchill Crocodile is called in normally (i.e. without flares)

Tactical Support Regiment
+ Designate Command Vehicle debuffs (speed, RoF, etc.) reduced
+ Field Recovery Operation now only calls in one Royal Engineer Recovery Squad

Vanguard Operations Regiment
+ Hawker Typhoon rocket strafe penetration slightly reduced (to match P-47) and AoE profile improved


* = These are commanders I don't have and therefore I cannot personally verify that they are working, but they should be as long as I didn't miss something.
** = These are commanders originally specific to the Theatre of War for year 1941

Note that there are many more abilties which have received more minor adjustments such as cost changes or what have you. The above list only includes the big changes, and I expect to add more of those over time.