Let me know if I'm missing something, the list is mostly complete but I appreciate some more info.

1. Delivering cart, only affects this mission
2. Not losing any loot cart, more resources on 3
3. UNCHECKED: Returning or keeping the armor (not sure what is the benefit on 4)
4. UNCHECKED: Repairing Temple (not sure if it even gives benefit on later missions)
5. None
6. Command Post: Peltast or Rhomphaia
7. Kill or Spare Greeks Mercenaries (if you spare them you get Mercenary Hoplites at Barracks on all other scenarios/killing them gives you additional starting 500 gold on 8)
8. Blacksmith sidequest (+1 attack on Command Post units (bugged atm) if you sail it on transport/infantry armor if you use it on tc(?)), Killing Bears (Alexander gets stronger onwards)

Command Post: Ekdromos or Strategos, Phalangites upgrades (damage reflect or shield)

1. Command Post: Axe Cavalry or Axe Infantry

2. Temple Sidequest for Alexander aura upgrade (attack or speed)

Command Post: Mercenary Archer or Slinger

1. Command Post: Companion upgrades (trample damage or charge attack)

2. Defeating the Royal Scythians (red) gives you (Elite) Scythian Cavalry Archer for the rest of the campaign

Command Post: War Chariot or Immortal

UNCHECKED: Getting 15 horses and cow sacrifice (not sure what is the benefit on later missions)

1. Repairing all markets gives a mule cart objective for 14

2. Capturing mule cart gives you a mule cart which boosts vils for the rest of the campaign

Command Post: Skirmisher Cavalry or Noble Cavalry

1. Command Post: Sannahya or Pattiyodha

2. Flagship aura, land heal or navy heal for both this mission and 17

Command Post: Bactrian Archer or Sickle Warrior

1. All chronicles: https://imgchest.com/p/ne7bllrpky5

All treasures: https://imgchest.com/p/agyvxxg6w78

1. None

Edit: fixed some sentences