There are many advantages of the area of effect jump drive. As JB said, simplicity of operation. It’s much simpler to group up around a carrier within radius x than to attempt entering its hangars one at a time. Factor in inexperienced pilots and griefers, and it becomes a disaster half the time.
In addition, it’s rather limiting to gameplay. In the area of effect model, the devs can assign an arbitrary maximum number of ships per carrier, whereas the internal volume of the carrier obviously has a hard cap. Also, capital ships would not be able to use a carrier’s jump drive if you had to fit inside. It would be much more optimal if capital ships could pool their jump drive strength into a faster fleet jump.
In Battlescape, players won’t mine or have any possessions to worry about except for their own ship, which can’t be stolen from them.
Edit: oops, didn’t read the second half of the post I mentioned…