Was it just his nature, or was he misled by bad advisers or counter-intelligence?
EDIT: Thanks for the answers and reading recommendations.
On top of the link provided by /carpenter I'd say that Intelligence played its part and much of this intelligence was linked to the Pinkerton agency. I recommend reading a quite interesting, and probably unique, book titled "The secret war for the Union". Relates all the intelligence efforts and sources of the Army of the Potomac with each of its commanding generals; by Intelligence I mean all intelligence in military terms, from agents, to scouts, use of cavalry for info gathering, balloons etc.
http://www.amazon.com/The-Secret-War-Union-Intelligence/dp/0395901367
I can't believe that no one else has tried to answer this question in over 13 hours, but here is a like to an old AskHistorians post about McClellan in which the same question is asked.
And based on my research on the internet, McClellan planned his battles with the philosophy of, to paraphrase Patton, 'A perfect plan implemented tomorrow is better than a good plan implemented today.' And while that may have been a good philosophy to take when running a railroad or training an army of fresh recruits, it was an absolutely terrible philosophy on the battlefield where events change faster than can be observed.
McClellan himself described his philosophy in quote that I lifted off of Wikipedia:
A lot of McClellan's inaction seems to stem from his personality. One of my favorite histories is Lincoln and His Generals, by T. Harry Williams. It's a classic, and is incredibly engaging. It focuses on Lincoln's interactions with his generals based on his correspondence, so more attention is paid to the generals who were flops. Great read.