I prefer side because they keep the weight lower and allow me to more easily swing a leg over.
When I tour I need extra space, so I end up with both.

I’ve been riding a big bike (mts1200) and I prefer the side bags. They provide some protection from me dropping it, they lower the centre of gravity a little bit, and they can technically hold more in them.

Using the top box would make me more top heavy than I already am.

I wish I could fit my helmet in the panniers, but its the price I must pay.