Suppose A is allied with B & C.
Each time A does a successful joint attack with either of them, the pair gets some points.
Based on these points some attribute gets stronger in their joint attacks.
Eg: Let the attribute which gets stronger be Defense value.
A has had 40 successful joint attacks with A; 30 successful joint attacks with C
So when A & B launch a joint attack together, their defense value rises by 4.
When A & C launch a joint attack together, their defense value rises by 3.
The mechanism is common, found in quite a few games.
I think it would be a great addition to this game

You can do other things with the ally points too - like, for example, put it in the ratings table.