I'm pretty sure he just only wanted to do one season. He might have too busy with Thor 2 coming out. I know actors usually have to travel around a lot for promo stuff and maybe his schedule just didn't line up.
In my understanding, I thought Eccleston, while appreciative of his fans, did not want to be known for just being The Doctor. Which I completely understand, because Doctor Who is very different than anything I've ever seen him in. He's a very dramatic, serious actor and tends to play darker roles.
There are also other Doctors that are also still alive that didn't make an appearance, such as Sylvester McCoy (who might be busy with Hobbit related stuff). I would have expected to see more of them at the end during the thank yous from cast, but whatevs. I was pleased with how it ended, even if it was CGI.