Justice Department Didn't Trust Rove
Murray Waas of The Villiage Voice has provided some insight into why a special prosecutor was appointed:
Justice Department officials made the crucial decision in late 2003 to appoint a special prosecutor to investigate the leak of the identity of undercover CIA officer Valerie Plame in large part because investigators had begun to specifically question the veracity of accounts provided to them by White House deputy chief of staff Karl Rove, according to senior law enforcement officials.
The Justice Department had good reason to question Rove’s honesty:
During his initial interview with the FBI, in the fall of 2003, Rove did not disclose that he had ever discussed Plame with Time magazine correspondent Matthew Cooper, according to two legal sources with firsthand knowledge of the matter. Federal investigators were also skeptical of claims by Rove that he had only first learned of Plame’s employment with the CIA from a journalist, even though he also claimed he could not specifically recall the name of the journalist.