As it is now, (EDIT:) a large portion of players actively avoid skeleton fleet battles, opting to wait for a fort to spawn. They are much harder than forts, more time consuming, and less rewarding (at least when comparing the time it takes to complete one). What incentive would make you want to do them again? Fewer waves? A limit of one ship per wave? More loot (with more time to collect it between waves)?
I'm not sure it needs an incentive, do you mean that you'd like more incentive to do them?
Personally I think they're a good additional choice on the seas if you fancy a challenge/are in an alliance/ fleet and have the time, but most will tackle skull forts because they're a little quicker and easier for single ships and crews, although you have the added risk of other crews attacking you.
We've tackled skellie fleets a couple of times and once caught the end of the battle and just had the captain's ship to sink.