I got kind of tired of a lot of the silly bugs that were simple XML changes so i decided to make some changes for myself. Figured out I could share my files with you guys in case someone else wanted the same changes as well. Below is a link to the file, and the changelog as well. Simply drag the zipped folder into your mods directory and enable mods ingame to use the fix.
I will probably keep updating this mod as i discover new bugs or for balance reasons etc. Also, I am very open to changes from the community so dont hesitate to reply to this thread if you have any bugs i have not weeded out yet, og balance suggestions.
Crusade 2.13 Sainon Bug Fix and Balance Changes v1.0
ChangeLog v0.1
-General Rearrangement of Tech Tree to be more similar to pre 2.13. Made Choices matter again and generally made tree more logical in its structure.
-Fixed Morale Buildings for Amphibious Ability, i. e. Healing Waters improvement and upgrades. Lowered morale bonus of buildings to 3, 4 and 5.
Removed adjacency bonus to affect pop and morale only
-Added Hive Buildings for Knowledgeable/Intuitive Races and added Precursor Nanite Cost to buildings. Rebalanced Raw Production to give 1, 2, and 3 per level.
-Gravitonics chain given to TimeTravellers only
-Moved Inherent Talent require Sensor Optimization instead of Energy Field Sensors
-High Capacity Hulls Require the same amount of research as the other techs in Zero-G Optimization
-Carriers not locked behind Hull Repair anymore
-Xeno Archeology chain now Requires Xeno Research
-Consulate Gives +10% Influence
-Scaling for levels on Influence Buildings changed to 5%
-Interstellar Embasy Starbase Module removed from Interstellar Finance Tech
-Trade Techs Changed around and fixed
-Synthetics Power Matrix buildings added again - now significantly increase pop cap. Pop Cap from tech reduced accordingly
-Production Center for Synthetics no longer colony Unique, but production bonus reduced from 25% to 5%. Poduction Center upgrades changed to 10%, 15% and 20%.
-Removed Xeno Manufacturing tech chain for Synthetics
-Synthetics Planetary Extractor now gives and recieves All Construction Neighbour bonuses
-Research modifier on Slave Factory improvements changed to 12.5% from 12%
-Research Collective moved to Xeno Research from Manufacturing tech for Synthetics
ChangeLog v0.2
-Colonial Bank No longer colony unique
-Banking Sector moved to Interstellar Banking Tech
-Banking Sector bonus changed from 50% to 25% and acjacency bonus changed from +3 to +2
-Financial Sector acjacency bonus changed from +4 to +2. Added Maintenance of 1
-Extreme Precursor Worlds now only produce +1 Raw Production instead of +10
ChangeLog v1.0
-Changed planet features giving bonus to Resistance to give the bonus to Ship Production instead - now it works for all military buildings such as
Military Academy and Planetary Defense System as well
-Changed planet features giving bonus to Social Construction to give bonus to both All Construction instead
-Changed planet features giving bonus to tourism to give bonus to Research instead as tourism is nonexistent in game
-Changed the Race Trait Popular to give bonus to social manufacturing instead of tourism, as tourism is pretty much nonexistent in game - it was 2 free points
-Chanaged description of Productive race trait to specify it gives bonus to both production types
-Banking Sector made available again.
-Financial Sector now upgrades from Banking Sector
-Changed adjacency bonus for research/manufacturing buildings for synthetics to 2.5% like it is for the xeno factories/labs
-Quantum Power Plant and the wonder Singularity Power Plant buildable for Synthetics
-Rare Minerals Extractor gives both research and manufacturing neighbour bonus
-Power matrix building and upgrades give adjacency bonus to All Manufacturing instead of just Social Manufacturing as Synthetics have no building providing
Social Manufacturing only
-Power Matrix building level scaling buffed from 1% to 2.5%
-Research Matrix building moved to Research Matrix tech from Integrated Research tech
-Research Array for Synthetics research bonus reduced from 12.5% to 10% - same as same tier manufacturing building
-Research Collective research bonus reduced from 10% to 7.5% - 5 research buildings instead of 4 require this, and Synthetics already get 2 flat bonus
research buildings per planet. Higher bonus earlier gives an even bigger edge
-Information Processor for Synthetics bonus reduced from 5% to 2.5% - same reasoning as above
-Removed Banking and Financial Sector for Synthetics. They have massive production and research bonuses already. Nerfing Eco power seems appropriate
-Removed Xeno Entertainment chain for Synthetics
-Interstellar Banking and Trade Focus techs moved to Age of War
-Moved Morale duilding techs to be available for for all races instead of requiring tourism/diplomatic trait
-Stadium moved to Popular Diversion
-Entertainment Network now requires Harmony Crystals instead of Arnor Spice
-Added 2 Harmony Crystal cost to Stadium
-Entertainment Capital now requires 3 Harmony Crystals instead of 1
-Financial Capital Aurorus Arboretum cost increased to 3 from 1
-Due to removal of tourism bonuses from traits/Planet features, buffed income from tourism modifiers from tech from +5%, +10, +15%, to +10%, +15%, +20%
-Buffed +tourism income from buildings after Port of Call to +25% and +50%
-Increase bonus per level for tourism buildings from 1% to 2.5%
-Increased bonus from Restaurant of Eternity to 75% from 10%, and bonus from level to 5% from 1%
-Removed unavailable tag from Amusement park
-Adjacency bonus for financial buildings reduced from 5% to 2.5%. Finance is REALLY strong with +5% adjacency bonus - easy +150 per turn on 15+ tile planets
-Moved Shadow Enforcers and Shadow Trade techs for Devouts to Age of War from Age of Expansion
-Removed upgrade requirement for quantum power plant to make it buildable. Reduced neighbour bonus from +4 to +2
-Research Coordination gives Space Laboratories. Tech chain for orbital space labs require Research Coordination now
-Innovation Complex gives +50% research from 20% considering it is an upgrade from Coordination Center which gives 25% bonus
-Manufacturing Starbase Modules added Xeno Industrialization chain for normal and synthetics
-Changed precursor Extreme world Raw Production bonus to +2, as the design intent from Stardoc seems to be +5 after checking official 2.13 patch files.
However, they forgot to change the bonus given after researching precursor studies techs. I changed it to +2 for all levels.
Enjoy! Any comments or critique is welcome 
I am by no means a game developer so my balance opinions may be waaay off!
Edit: Added some more changes, and uploaded new version.
Edit 2: Changed link to v1.0 and added the updated changelog