I've never been a fan of alliances and find them pointless. Most of the time it's "ahoy" "let's join an alliance" we raise the flag it's accepted and everyone carries on about their business.
Personally never been a fan of the way loot is given either.
My suggestion would be to split the loot even between the crews. The more crews in the alliance the less loot each crew gets.
Now I know some will be thinking well that makes alliances even more pointless. I would suggest as a means to make them worth while new voyages/quests are brought in which give a much greater yield but have a much higher difficulty almost to the point of being impossible as a single crew. Once the voyage/quest is complete the loot would have to be distributed evenly between the crews or you could turn on other crews to take all. Only those turning it get the actual loot.
I think the point to alliances should be to make crews work together towards a common goal rather than just raise a flag and continue on your way. Also this brings in an actual point to betraying an alliance if you so choose to