This can be rather interesting depending on the benefits. The biggest thing I could see is having this be a risk reward type deal. Like for instance let’s take a pairing like Aladdin and Jafar. Obvious Arch-Nemisis pairing. In battle you could have them gain bonuses for fighting each other. For example in this case you could have Aladdin be immune to Jafar’s charm in exchange for Jafar doing extra damage with his “Whirling Dervish” to Aladdin.
With a friendly rivalry lets keep using Aladdin and pair him with Flynn Rider. I know Flynn gets a disk from Aladdin but this is supposed to be different then friendship disks. Perhaps if they are on the same team they get a bonus to attack speed based on the energy they steal.
Lastly let’s go back to Jafar and his Arch-Rival in Scar. Again one gets a disk from the other but they could possibly get a bonus to damage based on how many status effects they afflict.
This adds another layer to the composition of teams and gives mechanical risk and reward for having teams that are on opposite sides of good and evil. Perhaps this idea is too far out there or too powerful but this is how I would work it.