I imagine most of the boss skipping will end in a few weeks with 2.0. Once all the boss fights reward comms there will be a reason to slaughter them again.
I think there will be more boss skipping. With a weekly cap of 50, many people are going to max out their comms before the week is out anyway, so why fight a boss that won't give any useful drops?
Also, since the new level 55 fp's will have a 50% chance to drop a crafting mat from the final boss, and since the final boss is one of the two bosses that will drop gear, I think after about two weeks you'll see people once again making speed runs skipping as much as they can.