It's a performance versus realism type thing - when your animations are sychronised, all the soldiers within the units are marching in step, the horses' tails all wag at the same time etc. This is less taxing on your PC than if you desychronise the animations - whereby each individual is animated 'separately' (or at least appears to be), making the unit look more realistic when moving. So - if your PC can handle it, desynchronising is the way to go for a more immersive experience.
Gah! You beat me to it, and said it better!
So, yeah, what he said!
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