This from a yahoo article:
It’s not weird that Meereen is attacked, because that’s happened before and it’ll happen again. It’s weird that Varys didn’t know Meereen was going to be attacked. It’s a little too convenient that he leaves the city shortly before it sets on FIRE.
“[Dany’s] fleet burning is quickly attributed to slave owners, which does not make much sense,” Ariskov writes. “They know she wants to conquer Westeros, and they know it is in their best interest that she leaves.
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That's a good point. OTOH, if Varys really knew, then wouldn't him leaving right at that moment be a dead giveaway that he had something to do with it? But that's what I thought about Little Finger when Joffrey got poisoned. He left right away yet nobody suspect that he had anything to do with it. Seems like both Varys and Little Finger would be prime suspects any time there is intrigue in the royal court. Doesn't make sense.