You can modify the bonuses but please make it balanced. So AoK Teutons civ bonus - TC +5 range is not even an option. However +1/+2 range in Castle/Imperial can be a consideration.
From my head, this is the list of removed bonuses and techs -
Team Bonuses :
Foot Archer +2 LOS.
Farms are built 100% faster. Maybe make it instantly like 1 or 2 seconds.
Mangonel line +1 range.
Spearman and Skirmisher +2 LOS.
Civ Bonuses :
Towers are built 33% faster. (Rest are taken by Sicilians)
Towers +1/+2 range in Castle/Imperial Age.
Fisherman works 15% faster.
Camel Rider +1/+1 armor.
Cavalry Archers +3 attack bonus vs buildings.
Start with +150 food.
2 Sheep spawns near TC upon reaching Feudal Age. Maybe improve it to all ages.
Galley line +1 attack.
Unique Techs
Obsidian Arrows. I personally don’t think it is broken by default as long as they don’t deal 12 damage to stone walls.
Mahouts. You can change the effect from War Elephant to any elephant units.
Boling Oil.
Madrasah.
Couriers.
Zealotry. Buff the old effect of +30 to +40 to make it stronger than Saracens.
“Old” Royal Heir - UU is trained 100% faster.
“Old” Paper Money - All team members get 500 gold.
“Old” Manipur Cavalry - Cavalry and elephants +6 attack bonus vs Buildings.
Berserkergang - UU regenerate HP.
Vineyards - Convert all food to gold.
Scutage - All team members get +15 gold for each existing military units.
Panokseon - Naval UU moves 15% faster.
Orthodoxy - Buff it to at least +4/+4 as Bengalis already have the bonus for free.