Pullin' out da back:

Advantages

Stealth - moves the baits away from the boat.
Time - Can pull with the big motor so all day runs are easier
Speed - can more easily obtain fast speeds at 2mph or greater and cover more water.
Spreads - It's easier to get more distance between the baits from the back with longer rods (at the widest point on the boat) and can also use planer boards.
It's easier to guide a fish around and through other lines than at the front with shorter lengths.
Cover more water, find more fish
With weights, you loose more fish due to shorter line and the weight giving them a leverage to pull off.
Netting is a problem from the front, easier from the back.
Pulling cranks is an all weather deal. It's effective in all wave conditions as long as you can take the discomfort.

Disadvantages:
Wider sweeping turns are required.
It's really a two man job if you're running the big motor as wind and waves will put you in a tight turn while handling a fish or putting out poles etc, unless you have the Co-Pilot/Ipilot.
More stuff, more $

That's pretty much it.

Wannabe...