The post by Ben Kuchera doesn't go into the details about why they're ending their run, but alas, it's over.
Ben, feel free to come post over here :)
See more here: http://penny-arcade.com/report/article/it-was-a-great-two-years-but-now-its-time-to-say-goodbye
EDIT: Penny Arcade proper posted some info about this, saying that it was to streamline things, but it isn't entirely clear.
http://www.penny-arcade.com/2013/12/06/changes

That is a sad to hear. I really enjoyed PAR during its run. I'll be interested to see where Ben ends up after this.
Interesting. I heard about the PA report but I never frequented it myself.
It's hard making money from doing the online vidya game news thing.
LLAP Ben!
This was a real shame. One of my favorite places to turn for news and editorials for the past year. But I was glad to see that Ben joined the staff at Polygon, as that is now my go-to gaming site!