It allows for more precise and less messy movement and targeting, and feels better and more natural, while taking nothing of value from the gameplay.
Decision-wise, it is the same: the goal is almost always to point toward a specific direction (which may not be fixed, for example when leading a target).
In the old scheme, I point at a direction and the ship does its best to turn as fast as possible with the right rotation speed (or stopped rotation) when aiming there.
In the new scheme, I have to manually make it accelerate and decelerate, and it is nearly impossible to get this perfect immobile alignment, which is rather important for precise flight and targeting. The impossibility to fly perfectly straight on a specific vector is particularly infuriating.
As far as the "twitch-gameplay" challenge goes, having to manually perform rotation and compensation feels messy to me, and most of all artificial. It is not unlike having bad latency in a FPS, or the old random movement added by some games when using scope sight.
I:B should not need this extra, artificial difficulty when positioning, prediction and flight are already requiring skill to perform well. Basically, it feels like I am turning the craft instead of actually flying the craft.
I personally also find it much more natural, as it is like that that several space/air sim games I played work, in addition to being close to the ever-popular FPS scheme (which from time to time also adds inertia in aiming).
With the new system, I just feel crippled, as if I had to manually pull flap cables instead of relying on a fly-by-wire control stick on a plane. Or if I was suddenly playing QWOP instead of actually running.
There may be edge cases where some forms of direct control over directional aim is superior, though I doubt they would appear in any but the most extreme super-agility dogfights.
Some may also find direct control more natural, particularly as it is how actual vehicles (particularly aircrafts) generally work in the first place, and it may be more suited for control sticks, so it would be best to have the choice. But if it does require only small amount of work to add the old scheme back, please consider it - even though calculating the optimal solution for a moving reticule may not be trivial.