The way I worked around this is giving some ships a returning armada like ability. So you can have dozens of captials but, it wont come from shipyard.
Example:
Gave the Advent colony a ability called
LightPSIBeaconTXT
entityType "CapitalShip"
ability:0 "AbilityPsiCapitalShipColonize"
ability:1 "AbilitySpreadWeaponDamage"
ability:2 "AbilityShieldRegenerate"
ability:3 "
AbilityLightPSIBeacon"
defaultAutoAttackRange "GravityWell"
defaultAutoAttackOn TRUE
prefersToFocusFire TRUE
autoJoinFleetDefault TRUE
canBomb TRUE
hasBombingLevels FALSE
baseDamage 40.000000
basePopulationKilled 1.550000
bombingFreqTime 10.000000
baseRange 3000.000000
bombTransitTime 12.000000
bombEffectCount 3
bombEffectAngleVariance 15.000000
bombEffectsDef
weaponType "Projectile"
burstCount 1
burstDelay 0.000000
muzzleEffectName "Weapon_PsiCapitalPlanetBombing_Muzzle"
muzzleSoundMinRespawnTime 0.100000
muzzleSounds
soundCount 1
sound "WEAPON_PSI_PLANETBOMB_MUZZLE"
hitEffectName "Weapon_PsiCapitalPlanetBombing_Hit"
hitHullEffectSounds
soundCount 3
sound "EXPLOSION_SUB4"
sound "EXPLOSION_SUB4_ALT1"
sound "EXPLOSION_SUB4_ALT2"
hitShieldsEffectSounds
soundCount 3
sound "EXPLOSION_SUB4"
sound "EXPLOSION_SUB4_ALT1"
sound "EXPLOSION_SUB4_ALT2"
projectileTravelEffectName "Weapon_PsiCapitalPlanetBombing_Travel"
mainViewIcon "MAINVIEWICON_CAPITALSHIP_PSICOLONY"
basePrice
credits 3500.000000
metal 450.000000
crystal 300.000000
slotCount 45.000000
BuildTime 75.000000
MaxHullPoints
StartValue 5500.000000
ValueIncreasePerLevel 70.000000
MaxShieldPoints
StartValue 11000.000000
ValueIncreasePerLevel 175.000000
HullPointRestoreRate
StartValue 3.500000
ValueIncreasePerLevel 0.100000
ShieldPointRestoreRate
StartValue 17.000000
ValueIncreasePerLevel 0.200000
ArmorPointsFromExperience
StartValue 3.000000
ValueIncreasePerLevel 0.375000
maxMitigation
StartValue 0.82
ValueIncreasePerLevel 0.01111
MaxAntiMatter
StartValue 650.000000
ValueIncreasePerLevel 35.000000
AntiMatterRestoreRate
StartValue 3.850000
ValueIncreasePerLevel 0.100000
CultureProtectRate
StartValue 0.300000
ValueIncreasePerLevel 0.050000
NameStringID "IDS_CAPITALSHIP_PSICOLONY_NAME"
DescriptionStringID "IDS_CAPITALSHIP_PSICOLONY_DESCRIPTION"
picture "CAPITALSHIPPICTURE_PSICOLONY"
Prerequisites
NumResearchPrerequisites 0
roleType "COLONY"
statCountType "CapitalShipUtility0"
numRandomDebrisLarge 4
numRandomDebrisSmall 18
numSpecificDebris 0
armorType "CapitalShip"
hudIcon "HUDICON_CAPITALSHIP_PSICOLONY"
smallHudIcon "HUDICONSMALL_CAPITALSHIP_PSICOLONY"
infoCardIcon "INFOCARDICON_CAPITALSHIP_PSICOLONY"
minZoomDistanceMult 1.250000
NumWeapons 2
Weapon
WeaponType "Projectile"
damageEnums
AttackType "CAPITALSHIP"
DamageAffectType "AFFECTS_SHIELDS_AND_HULL"
DamageApplyType "BACKLOADED"
DamageType "ENERGY"
WeaponClassType "PLASMA"
DamagePerBank:FRONT 1000.000000
DamagePerBank:BACK 1000.000000
DamagePerBank:LEFT 1000.000000
DamagePerBank:RIGHT 1000.000000
Range 90000.000000
PreBuffCooldownTime 5.000000
CanFireAtFighter FALSE
SynchronizedTargeting FALSE
PointStaggerDelay 0.400000
TravelSpeed 2000.000000
Duration 0.000000
WeaponEffects
weaponType "Projectile"
burstCount 2
burstDelay 0.600000
muzzleEffectName "Weapon_PsiCapitalPlasmaHeavy_Muzzle"
muzzleSoundMinRespawnTime 0.100000
muzzleSounds
soundCount 3
sound "WEAPON_PSICAPITALPLASMAHEAVY_MUZZLE"
sound "WEAPON_PSICAPITALPLASMAHEAVY_MUZZLE_ALT1"
sound "WEAPON_PSICAPITALPLASMAHEAVY_MUZZLE_ALT2"
hitEffectName "Weapon_PsiCapitalPlasmaHeavy_Hit"
hitHullEffectSounds
soundCount 1
sound "WEAPONIMPACT_ENERGYHEAVY_HITHULL"
hitShieldsEffectSounds
soundCount 1
sound "WEAPONIMPACT_GENERICHEAVY_HITSHIELDS"
projectileTravelEffectName "Weapon_PsiCapitalPlasmaHeavy_Travel"
Weapon
WeaponType "Projectile"
damageEnums
AttackType "CAPITALSHIP"
DamageAffectType "AFFECTS_SHIELDS_AND_HULL"
DamageApplyType "BACKLOADED"
DamageType "ENERGY"
WeaponClassType "LASERPSI"
DamagePerBank:FRONT 500.000000
DamagePerBank:BACK 500.000000
DamagePerBank:LEFT 500.000000
DamagePerBank:RIGHT 500.000000
Range 100000.000000
PreBuffCooldownTime 2.100000
CanFireAtFighter FALSE
SynchronizedTargeting FALSE
PointStaggerDelay 0.500000
TravelSpeed 4000.000000
Duration 0.000000
WeaponEffects
weaponType "Projectile"
burstCount 6
burstDelay 0.200000
muzzleEffectName "Weapon_PsiCapitalLaserLight_Muzzle"
muzzleSoundMinRespawnTime 0.100000
muzzleSounds
soundCount 3
sound "WEAPON_PSICAPITALLASERLIGHT_MUZZLE"
sound "WEAPON_PSICAPITALLASERLIGHT_MUZZLE_ALT1"
sound "WEAPON_PSICAPITALLASERLIGHT_MUZZLE_ALT2"
hitEffectName "Weapon_PsiCapitalLaserLight_Hit"
hitHullEffectSounds
soundCount 1
sound "WEAPONIMPACT_ENERGYLIGHT_HITHULL"
hitShieldsEffectSounds
soundCount 1
sound "WEAPONIMPACT_GENERICLIGHT_HITSHIELDS"
projectileTravelEffectName "Weapon_PsiCapitalLaserLight_Travel"
m_weaponIndexForRange 0
mass 7500.000000
ShieldMeshName "Shield_PsiColony"
maxAccelerationLinear 200.000000
maxAccelerationStrafe 20.000000
maxDecelerationLinear 600.000000
maxAccelerationAngular 3.000000
maxDecelerationAngular 12.999996
maxSpeedLinear 1300.000000
squadTypeEntityDef:0 "SquadPSIGunshipC"
squadAntiMatterCost:0 75.000000
squadTypeEntityDef:1 "SquadPSIGunshipB"
squadAntiMatterCost:1 100.000000
NumSoundsFor:ONATTACKORDERISSUED 3
SoundID "CAPITALSHIP_PSICOLONY_ONATTACKORDERISSUED_0"
SoundID "CAPITALSHIP_PSICOLONY_ONATTACKORDERISSUED_1"
SoundID "CAPITALSHIP_PSICOLONY_ONATTACKORDERISSUED_2"
NumSoundsFor:ONCREATION 1
SoundID "CAPITALSHIP_PSICOLONY_ONCREATION"
NumSoundsFor:ONGENERALORDERISSUED 3
SoundID "CAPITALSHIP_PSICOLONY_ONGENERALORDERISSUED_0"
SoundID "CAPITALSHIP_PSICOLONY_ONGENERALORDERISSUED_1"
SoundID "CAPITALSHIP_PSICOLONY_ONGENERALORDERISSUED_2"
NumSoundsFor:ONSELECTED 3
SoundID "CAPITALSHIP_PSICOLONY_ONSELECTED_0"
SoundID "CAPITALSHIP_PSICOLONY_ONSELECTED_1"
SoundID "CAPITALSHIP_PSICOLONY_ONSELECTED_2"
NumSoundsFor:ONSTARTPHASEJUMP 1
SoundID "CAPITALSHIP_PSICOLONY_ONSTARTPHASEJUMP_0"
MeshName "CapitalShip_PsiColony"
ExhaustParticleSystemName "Exhaust_PsiColony"
ExplosionName "CapitalShip0"
CommandPoints
StartValue 4.200000
ValueIncreasePerLevel 0.250000
weaponCooldownDecreasePerc
StartValue 0.000000
ValueIncreasePerLevel 0.020000
weaponDamageIncreasePerc
StartValue 0.000000
ValueIncreasePerLevel 0.060000
HyperspaceChargingSoundID "HYPERSPACE_CHARGEUP"
HyperspaceTravelSoundID "HYPERSPACE_TRAVEL"
EngineSoundID "ENGINE_PSICAPITALSHIP"
formationRank 2
minShadow 0.000000
maxShadow 0.500000
Ability file:
Calls help and is aided by three ships. Works really well also been exploring homeworld type of play where your always on a move.
TXT
entityType "Ability"
buffInstantActionType "SpawnShipsAtPlanet"
instantActionTriggerType "AlwaysPerform"
spawnShipsLevelCount 2
spawnShips
minFleetPoints 35.000000
maxFleetPoints 40.000000
requiredShipCount 0
randomShipCount 3
randomShip
type "FrigateLightPsiInterceptor"
weight 1
randomShip
type "FrigatePsiMediumInterceptor"
weight 2
randomShip
type "FrigateHeavyPSI Interceptor"
weight 3
spawnShips
minFleetPoints 50.000000
maxFleetPoints 55.000000
requiredShipCount 0
randomShipCount 3
randomShip
type "FrigateLightPsiInterceptor"
weight 1
randomShip
type "FrigatePsiMediumInterceptor"
weight 2
randomShip
type "FrigateHeavyPSI Interceptor"
weight 3
spawnShipsArrivalDelayTime 10.000000
spawnShipsHyperspaceSpawnType "FleetBeacon"
needsToFaceTarget FALSE
canCollideWithTarget TRUE
moveThruTarget FALSE
isUltimateAbility FALSE
maxNumLevels 2
levelSourceType "FixedLevel0"
aiUseTime "OnlyWhenTakingDamage"
aiUseTargetCondition "Any"
isAutoCastAvailable TRUE
isAutoCastOnByDefault False
pickRandomPlanetToExploreForAutoCastTarget FALSE
ignoreNonCombatShipsForAutoCastTarget TRUE
onlyAutoCastWhenDamageTakenExceedsPerc 0.000000
isPassive FALSE
antiMatterCost
Level:0 60.000000
Level:1 120.000000
Level:2 0.000000
cooldownTime
Level:0 75.000000
Level:1 150.000000
Level:2 0.000000
researchPrerequisites
NumResearchPrerequisites 0
nameStringID "IDS_ABILITY_PSIBEACON_NAME"
descStringID "IDS_ABILITY_PSIBEACON_DESCRIPTION"
hudIcon "HUDICON_ABILITY_FLEETBEACON"
smallHudIcon "HUDICON_ABILITY_FLEETBEACON"
infoCardIcon ""
Hope it helps.