Take PVP offline and dissolve all alliances while the changes are made.
Make Alliances sizes Mandatory membership within 10% size of each other. So, if everyone tries to jump in one Alliance on the first day, freeze membership until all other alliances are within 90% capacity of largest.
Make each Alliance get bonuses on a specific class / color type.
Give each Alliance a specific advantage over one of the other alliances
Example:
Dark Order 20% stronger with Undead, Daemon, Monster, Doom, Naga classes. 15% damage increase from members of the Golden Forge.
Bright Empire 20% stronger with Elemental, Fey, Elf, Merfollk, Mystic Construct classes. 15% damage increase from members of the Wild Horde.
Enchanted Grove 20% stronger with Beast, Centaur, Dwarf, Gnome, Dragon, Stryx classes. 15% damage increase from members of the Dark Order.
Wild Horde 20% stronger with Wildfolk, Orc, Taurus, Naga, Raksha, Giant, Urska, Wargare. 15% damage increase from members of the Enchanted Grove.
The Golden Forge 20% stronger with Divine, Human, Knight, Rouge, Mech Classes. 15% damage increase from members of the Bright Empire.
Immortals, Bosses and rainbow Dragons would receive no Alliance bonuses.