There was another topic on the same subject just a few days ago.
The general consensus from that topic was that there was no need to merge the skills, just make them better, more worth using.
I'd argue that once they're worth using, there's a good reason to keep them separate: A warrior character will tend to have high Phys. armor, but lower magic armor, so they might want to save points by pumping their Magic Armor ability to boost it to a reasonable amount and leave Physical alone.
It's spending ability points to compensate for the weakness of stats.
