Alpha 0.4
Org damage was excessive so toned that down. Playing a bit with weather I decided to remove the carrier flight penalty, it was causing issues. Also made CVF worthwile again - they kill enemy planes, but not anything else. Also snuck in some slight changes to naval warfare(toned down base hit rates). Nerfed the max ammount of land based aircraft that can join naval battles and strikes. I think naval strike damage might still need to be upped slightly.

General:
Removed "carrier traffic penalty" from weather and night - carrier planes fly all the time, carrier plane sortie rest doubled to compensate(so they still make 3 sorties/day).
Removed naval strike attack and targeting from CVF. This causes them to go into air superiority mode instead of naval strike mode - they will hunt down enemy fighters and bombers instead of strafing enemy ships.

NAir
COMBAT_ONE_ON_ONE_CHANCE = 0.6 (0.8)
COMBAT_SITUATION_WIN_CHANCE_FROM_STATS = 0.5 (0.3)
COMBAT_SITUATION_WIN_CHANCE_FROM_GANG = 0.1 (0.3)
COMBAT_ATTACK_PASSES_AT_ONCE = .01 (1)
CARRIER_HOURS_DELAY_AFTER_EACH_COMBAT = 8 (4)
NAVAL_STRIKE_DAMAGE_TO_STR = 5 (4)
NAVAL_STRIKE_DAMAGE_TO_ORG = 2 (4)
NAVAL_STRIKE_AIR_VS_AIR_PASS_CHANCE = .9 (1)
NAVAL_COMBAT_EXTERNAL_PLANES_JOIN_RATIO = 0.02 (0.05)
NAVAL_COMBAT_EXTERNAL_PLANES_JOIN_RATIO_PER_DAY = 0.02 (0.05)

NNavy
COMBAT_BASE_HIT_CHANCE = 0.075
COMBAT_MIN_HIT_CHANCE = 0.005
COMBAT_MAX_GROUPS = 5
EXPERIENCE_FACTOR_NON_CARRIER_GAIN = 0.02

Alpha 0.3B
Had slipped on some numbers, but when testing a more even battle they showed some weakness. Still think damage caused by aircraft is to low so will probably have to bump it higher. AA Targeting was the one that was very wrong in the previous version.

Changes this time:
NAVAL_STRIKE_TARGETTING_TO_AMOUNT = 0.2 (.15)
NAVAL_STRIKE_DAMAGE_TO_ORG = 4 (1)
ANTI_AIR_TARGETTING_TO_CHANCE = 0.15 (.3)
EXPERIENCE_FACTOR_CARRIER_GAIN = 0.02 (.1)

Increasing overall bloodyness of naval air warfare (Aircraft were having to little impact). Also reduced carrier exp gain so there more in line with other ships(Ie not lvl5 after one battle). Upped evasion cap to help preserve some screens. Lowered standard naval combat damage a little. AAA has gotten a decent boost, planes will be lost and damage will be dealt.
Looked over CAS/NAV/TAC stats. Damage now increases because of higher accuracy instead of both accuracy and attack. Overall slightly reduced average damage for all except CAS. However crit damage increased.

Defines changed:
NAVAL_STRIKE_DAMAGE_TO_STR = 4 (was 2)
AIR_AGILITY_TO_NAVAL_STRIKE_AGILITY = .01 (was .02)
MAX_EVASION_BONUS = 0.2 (was 0.1)
ANTI_AIR_TARGETTING_TO_CHANCE = 0.2 (was .15)
ANTI_AIR_ATTACK_TO_AMOUNT = 0.007 (was .003)
EXPERIENCE_LOSS_FACTOR = 0.50 (was 1)
EXPERIENCE_FACTOR_CARRIER_GAIN = 0.01 (was .1)
COMBAT_DAMAGE_TO_STR_FACTOR = 1.4 (was 1.6)
MIN_TRACTED_ASSIST_DAMAGE_RATIO = 0.15

Added a title picture

Initial release
Changes to 00_defines.lua (the part that actually fixes the bug)
COMBAT_ONE_ON_ONE_CHANCE = 0.8 (0.6) - Stats matter more than numerical adv.
COMBAT_ATTACK_PASSES_AT_ONCE = 1 (0.1) Slight increase in kill rates
NAVAL_STRIKE_AIR_VS_AIR_PASS_CHANCE = 1 (0.5) Anything less than 1 causes the naval air decimation bug
NAVAL_STRIKE_TARGETTING_TO_AMOUNT = 0.15 (0.3) Reduce damage dealt
NAVAL_STRIKE_DAMAGE_TO_STR = 2 (3) Reduce strength damage
NAVAL_STRIKE_DAMAGE_TO_ORG = 1 (3) Reduce org damage
AIR_AGILITY_TO_NAVAL_STRIKE_AGILITY = 0.02 (0.01) Increase importance of agility when doging aa
NAVAL_STRIKE_DETECTION_BALANCE_FACTOR = 0.2 (0.7) Decrease max frequency of naval strikes
ACCIDENT_CHANCE_BALANCE_MULT = 1 (0.5) Double accident frequency
NAVAL_COMBAT_EXTERNAL_PLANES_JOIN_RATIO_PER_DAY = 0.05 (0.2) Reduce max land bombers to join naval combat each day
ANTI_AIR_TARGETTING_TO_CHANCE = 0.15 (0.07) Increase hit chance of ship AA
ANTI_AIR_ATTACK_TO_AMOUNT = 0.003 (0.005) Reduce ship aa damage

Aircraft rebalance (To fix some long standing imbalances):
NAV: Naval strike damage nerfed
CAS: Naval strike damage buffed
TAC: Naval strike hit chance nerfed
FGT: Naval strike hit chance buffed, damage nerfed
OHKA: lower AGI and defence(easier to shoot down) but increased naval strike hit rate.