Ships assigned using a direct order via "Assign Task..." no longer count against towards the total strength of ships given to the assignment, except for "Capture". The effect is that directly assigning a ship to a task is less likely to cause other ships to be reassigned away from it.
After some playing around, I find I'm not actually looking forward to this change - I find that I'm using the current behavior a fair bit. The most common use case is when I see a single enemy frigate or fighter squadron breaking past the main lines of combat to get to a nav point in the rear, and I want to assign a single, say, heavy fighter squadron to go hunt it down *before* it captures a comm array and puts another thirty points of enemy reinforcements on the field. But I don't want to take more than that one ship I've assigned out of, well, whatever random thing it happens to be doing.
(Yes, this costs me two command points just to give a specific order to a specific ship; took me a while to realize I had to create the order to harass / strike / whatever and *then* assign a specific vessel to it. But totally worth it to prevent an enemy from ever holding my comm array; even a momentary capture of one of those can make a big swing in how the battle's going.)
...Though, come to think of it, that may not be quite so necessary once we have decent weightings for proximity-based priority; the main reason I'd assign a specific ship to that is that, usually, there's only one ship that could possibly respond in time anyway.
Perhaps a more intuitive model would be one where, instead of assigning a specific ship to a specific pre-existing fleet-wide task, one could give a specific ship its own particular task (with task graphic tied to that one ship instead of its target)? That would accomplish the same goal as this change (allow one to add "extra" ships to a fleet-wide task), while still allowing my use-case of wanting to send a single fast ship to intercept a particular enemy vessel.
[edit] And even allow the specific exception called out in this change to work, too - you'd just assign a ship to capture a nav point, and
not create a fleet-wide capture-this-nav-point task. [/edit]