You can edit the .xml on your Sovereign to restore Organized, if you are feeling the need... I've been using notepad.
<SelectedAbilityBonusOption>Sovereign_Ability_Logistics_Organized</SelectedAbilityBonusOption>
Look under Documents/My Games/Elemental/Units to find the .xml stats for your custom Sovereign.
I forget now how much the ability was worth (I'm thinking 10 points) in case you want to balance your character accordingly.
This still works under 1.09n. Hopefully they at keep it in place so the Modders can use it if they so wish.
And yes, it has been removed because it may be too powerful (especially if you put some move 1 units with a move 6+ Sovereign, such as Catapults).