What likely happened is that he used his real name very early on in the project since at the time there was no real reason to hide, but as things progressed he got spooked at some point and started being very careful. At that point however it was already to late to use a pseudonym without raising even more suspicion; imagine saying don't call me "Satoshi Nakamoto" any more, from this day fourth I shall be known as "Little John" its like announcing to everyone my real name is actually "Satoshi Nakamoto" and I dun messed up.

What most people say was that he was very careful towards the end, and assumed he had always been careful...clearly on day one i would have been hard to predict that bit coins would be where they are today.