Here is a guide on the new Alliance Perks introduced in Update 4.0:
Steal More Supplies Steal More Red Mercury Steal More Hexium - These Perks increase the amount of resources available for capture when destroying an enemy Base.
Medal Protection - This Perk reduces the number of Medals lost when defeated in combat, down to a minimum of 2.
Hexium Event Raid Point Bonus Missile Strike Event Raid Point Bonus - These Perks add .1 per rank to the multiplier during an event
Reduce Part Donation Wait Time Reduce Donation Wait Time - These Perks reduce the wait time on donating Troops and Parts to fellow Alliance members.
Troop Rearm Bonus - This Perk increases the number of Troops returned to you after combat.
Increase Troop Donation Capacity - This Perk allows for additional Troop donations to members of your Alliance.
Upgrade Donated Troops - This Perk increases the research level of Troops donated, up to a Troop's maximum available rank. This Perk helps ensure that all members in your Alliance are donating powerful Troops for combat.
Upgrade Alliance Gifting - This Perk increases the quantity of rewards inside an Alliance Gift Crate. Alliance Gift Crates are sent automatically to all members of your Alliance when you purchase Power Cells in the store. The item level of the crate is determined by the number of Power Cells you purchase. Item level determines the quality of items in a crate, while Perk level determines the quantity of items found.