What do you think Dany should have done differently to prevent chaos in Meereen?

Well, I address this to some extent in my essay on Dany’s campaign.

Dany’s mistakes were threefold:

1. She took *all* of the Unsullied out of Astapor, leaving her new government without a military to support it. As a result, it was easily toppled by any demagogue with a ready story and a knack with a cleaver. Slavery returned to Astapor (somewhat), and Astapor itself completely undermined her foreign policy, dragging her into a war she didn’t want to fight.
2. She left the Wise Masters in charge of Yunkai. By taking the slaves but leaving the masters, who retained most of their wealth and all of their political power, Dany created a number of problems. By having the slaves with her, she weakened her military readiness, made logistics a nightmare, and created the preconditions for epidemic disease. By leaving the masters, who both had a grudge against her and an economic, social, and political imperative to wipe out her experiment, she left an enemy in her rear who promptly re-armed, pulled together an anti-emancipation coalition, and reconquered Astapor, beginning to undo her revolution even before they laid siege to Meereen.
3. She tried to have things both ways in Meereen, liberating the slaves and giving them political power, but keeping the Great Masters intact with control over all the economic resources. The Masters reacted to what they saw as an existential threat to their identity by forming a terrorist group designed to undermine her government, make an example against freedmen and women who were active politically or trying to better themselves economically, and drive her out of Meereen through attrition. 

So if I were advising Dany, I first would have told her to leave a handful of centuries of the Unsullied behind as a garrison in Astapor. She’d still have more than enough infantry, and her council of three would have been able to remain in power as Cleon the Would-Be rotted in the cells awaiting trial for treason. Second, I would have told her to destroy the Wise Masters of Yunkai as she did the Good Masters of Astapor, and give the city (minus resupply for the army) to the freedmen, while leaving behind another couple of centuries of Unsullied to support the new government. This would have meant that Dany would have two allies to her south when she marched on Meereen, and greatly improved the logistics situation when the Meereenese begin poisoning the wells and cutting the trees. Third, I would have told her to destroy the Great Masters of Meereen save for the shavepates. This would have removed the constituency for the Sons of the Harpy to form, and would have allowed the freedmen of Meereen to become economically self-sufficient through redistribution of the Masters’ estates. 

From this point on, whatever else Dany chose to do or had to deal with, she’d at least have the major cities of Slaver’s Bay united and loyal to her cause. If she wants to stay in Meereen, great, she’s got two cities to work out trade deals with and if New Ghis or Volantis want to start trouble, she’s got two allies to back her up and there’s no Yunkai to coordinate her opponents. If she wants to march west, then she only has to deal with disciplined Unsullied rather than tens of thousands of starving, plague-ridden refugees.