What are you having issues with? There is not much difference in modding between 2.0 and 2.1, some scheme files changed the layout of some files ect. but nothing I would call major.

If you're using mods made for GC3 2.0 or earlier it's highly unlikely that they will work, as there were extensive changes for Crusade.  Horemvore has reworked many if not all of his mods for Crusade, but not all mod authors have.

Which mods specifically are you having problems with?

Edit: I see the OP mentioned the tech specializations, TrevorBlue is working on updating his tech tree editor which will make it much much easier to create a tech tree without specializations, but we'll have to wait for that.

Look for a post here in the modding section titled "[Collection] Horemvore's Crusade Mods" for Horemvore's updated mods. (I'd provide a direct link but the Stardock forums are giving me problems in that regard lately).

As far as I know Gauntlet is still working on updating his mod.  I don't know about SaladinTheKind.

 Tried Horemvore's Crusade Mods and received some errors on startup. Here are the errors I got. 

C:\Users\Brian\Documents\My Games\GC3Crusade\Mods\Star Trek Crusades\Game\GalCiv3AIDefs.xml(978,35): error: 

no declaration found for element 'AIContactHumanRandomRangeMin'

C:\Users\Brian\Documents\My Games\GC3Crusade\Mods\Star Trek Crusades\Game\GalCiv3AIDefs.xml(1503,15): error: 

element 'AIContactHumanRandomRangeMin' is not allowed for content model '(MaxRallyPointFleetMeetupDistance,NewRallyPointFleetMeetupRange,MaxRallyPointInvasionPrepDistance,NewRallyPointInvasionPrepRange,BattleRatingWeaponMod,BattleRatingDefenseMod,BattleRatingHitPointsMod,DangerPathCheckRadius,DangerBellCurveTargetDivisor,SendFleetsOnWarPathChance,WartimeFocusSectorRadius,WatimeFocusSectorTargetBonus,MinShipCountWeightMod,PlanetInDangerDefenseShipMod,PlanetInDangerAttackShipMod,IdleReturnHomeCount,IdleConsiderForRetireCount,DifficultyRule+,ResearchCostDivisor,PlanetTraitStatSamplingFlatBonus,GovernorWorstAcceptedScore,BaseOpenBoardersTreatyValue,OpenBoardersXenophobicValueMod,BaseExplorationTreatyValue,ExplorationXenophobicValueMod,BaseEmbargoTreatyValue,BaseDeclareWarOnThirdTreatyValue,BaseCulturalTreatyValue,BaseFreeTradeTreatyValue,BaseSlaveTreatyValue,PeaceTreatyModValue,NegativePeaceTreatyRelationModValue,PositivePeaceTreatyRelationModValue,AllianceModValue,NegativeAllianceRelationModValue,PositiveAllianceRelationModValue,NonAggressionModValue,NegativeNonAggressionRelationModValue,PositiveNonAggressionRelationModValue,NegativeEmbargoRelationModValue,PositiveEmbargoRelationModValue,NegativeDeclareWarOnThirdRelationModValue,PositiveDeclareWarOnThirdRelationModValue,DurationalCreditsModValue,BaseColonyTradeValue,ColonyProductionPointsMod,ColonyNumBuildingsMod,BaseStarbaseTradeValue,ConstructionPointValue,PairedStarbaseResourceValue,PairedAscensionGateValue,SweetenThePotAscVictoryBuyPairedAscensionGateValue,MyOwnColonyCostModValue,PredictionCultureFlipNumTurns,MyShipTradeCostModValue,TheirShipTradeCostModValue,TechTradeCostModValue,TechTradeLeadupCostModValue,ExclusiveTechLeadupValue,EleriumTradeModValue,DurantiumTradeModValue,AntimatterTradeModValue,PromethionTradeModValue,ThuliumTradeModValue,YouCantFoolMeGrudgeModValue,MinRelationScoreBeforeDeclareWar,FactionPowerModWhenCheckingForWar,BattlePowerModWhenCheckingForDanger,WarEnduranceModForInvasionWin,WarEnduranceModForInvasionLoss,WarEnduranceGainedFromFleetVi

C:\Users\Brian\Documents\My Games\GC3Crusade\Mods\Star Trek Crusades\Game\GalCiv3GlobalDefs.xml(1000,26): error: 

no declaration found for element 'MusicWinningPercent'

C:\Users\Brian\Documents\My Games\GC3Crusade\Mods\Star Trek Crusades\Game\GalCiv3GlobalDefs.xml(1001,35): error: 

no declaration found for element 'MusicWinningTriggerTurnCount'

C:\Users\Brian\Documents\My Games\GC3Crusade\Mods\Star Trek Crusades\Game\GalCiv3GlobalDefs.xml(1002,25): error: 

no declaration found for element 'MusicLosingPercent'

C:\Users\Brian\Documents\My Games\GC3Crusade\Mods\Star Trek Crusades\Game\GalCiv3GlobalDefs.xml(1003,34): error: 

no declaration found for element 'MusicLosingTriggerTurnCount'

C:\Users\Brian\Documents\My Games\GC3Crusade\Mods\Star Trek Crusades\Game\GalCiv3GlobalDefs.xml(1351,19): error: 

element 'MusicWinningPercent' is not allowed for content model '(MaxNumTurns,CreditsAndPowerCap,DefaultTileMoveCost,MinTileMoveCost,ExploreTileRandomRange,MinManufacturingSlider,StartImprovementLevel,StarbaseModuleSalvageMultiplier,ShipyardMaxSponsorCount,ShipyardSalvageMultiplier,BaseStarbaseDef,VigilantStarbaseDef?,BaseShipyardDef,GamePacingPacingDef,ResearchRatePacingDef,BaseMiningBaseBuildTime,NonStackingEffects*,ManufacturingSliderLowerScalePoint?,ResearchSliderLowerScalePoint?,TaxesSliderLowerScalePoint?,DefaultEjectTile,RushCostMultiplier,CapitalImprovement,CivilizationCapitalImprovement?,IdeologyTraitBaseCost,CoercionForgiveness,CoercionMaxPenalty,PopulationToProductionExponent,PopulationToProductionMultiplier,GlobalTriggers*,GlobalCombatMods*,GlobalFactionMods*,GlobalColonyMods*,GlobalInterColonyMods*,GlobalCapitalColonyMods*,GlobalAsteroidMods*,TradeRouteInitiatorMods*,TradeRouteRaidMods*,TradeRouteRaidPathMods*,WarWithFavoredCivMods*,DefenseDamageWeaponMod,MinimumDamage,ApprovalToGrowthCurve,ApprovalToProductionCurve,ApprovalToInfluenceCurve,ApprovalToResistanceCurve,ApprovalHappyThreshold,ApprovalContentThreshold,InfluenceMinToClaim,InfluenceRadiusRoot,InfluenceBellCurveTargetDivisor,InfluenceFactorOnTakeover,InfluenceFalloff,GrowthDecay,DiplomacyViewCameraMovementEasingCurve,EngineTrailWidthCurve,NumFreeStarbases,AdditionalCostPerStarbase,RequiredStarbaseSpacing,TacticalBattleArenaSize,TacticalBattleMinHitChance,BattleMinFireDelay,BattleMaxFireDelay,MinShipPopulation,DefaultShipPopulation,ReservedColonyPopulation,MaxPopulationSourceDistance,LoadTransportPopupWndDisplayMultiplier,LoadTransportPopupWndScrollbarNumStepsMultiplier,GraphVerticalRangePadding,GraphMaxNumFactionsToDisplay,MainMapGraphLineThickness,MainMapGraphMaxTurnsRange,GraphsScreenGraphLineThickness,TechTreeLineInsetDistance,TechTreeHorizontalSpacing,TechTreeVerticalSpacing,TechTreeClusterSpacing,TechTreeScreenCenterX,TechTreeScreenCenterY,TechTreeMarginX,TechTreeMarginY,TechTreeCenterViewOnSelect,TechTreeIsDraggable,TechTreeMomentum,Te

My mods only work with 2.1.4 (Beta Opt-In)

Oh alright. I will get the opt-in. Thanks Horemvore

Ohm... I see it's been busy here.
Well for me I have several mods from Nexus but one mine which is mostly my unique faction with ship style etc.
I got these 2 errors multiple times:

error: 

no declaration found for element 'ObjectGfxConfig'

error: 

element 'ObjectGfxConfig' is not allowed for content model '(ShipDesign,ThumbnailOverride?)'

I had no issues before the Crusades also my custom faction(xml based) does not appear in game anymore.
I have moved all mods from old GC3 folder to new GC3 Crusades one.

Probably I will have to create my custom race again using Crusades xml file but I have no idea how to work with new tech tree.
I'm using Terran Tech Tree and use the TechTree editor to remove specializations now this is not possible at the moment.

Another issue I had unrelated to Crusades was that I wanted to create a terraformed Mars. I did all correctly, I had the files in GC3 folder under Program Files and not Documents, I used /atlasgen worked correctly only once, after that when I made some fine tuning on map, Mars turned a blue globe 0 PQ. All files were checked again and again xml etc. I even removed all other mods for testing purposes no change. 

@alphaprior - I don't believe you can directly create tech trees as they are now based on racial traits. How that works I don't know.