It was deliberate... it caused the defendants to burn time and money.
Under Federal Rule of Civil Procedure 8(a)(2), a complaint is only required to have "a short and plain statement of the claim showing that the pleader is entitled to relief." Prior to 2007, this had been interpreted by the U.S. Supreme Court to mean that the complaint would only fail if, on its face, the pleader could prove no set of facts that would entitle him to relief.
In 2007, the Supreme Court tightened up these standards in the two cases Judge Pechman referenced in her ruling. Now, to comply with Rule 8, a pleader must allege enough specific facts in support of his claim so that relief is more than speculative. In other words, "Staples, you infringed my patent, you bastards!" no longer cuts the mustard.
Prior to 2007, though, the type of boilerplate pleading that Paul Allen's lawyers submitted was just fine. They continued to get away with it until, as now, someone decided to call them out on it. The suggestion probably came from a summer associate who mentioned, "argue Twombly and Iqbal" in passing to his boss.
Just doing my part to correct some of the rampant legal illiteracy on /.