Originally Posted By: Prometheus
Rumors:

-Eccleston and Barrowman did not get along. John likes to be a big jokster/flaming queen on set. Eccleston is a very serious actor. You do the math.

-Keith Boak, a director for an entire block of episodes, treated Eccles like he didn't know how to act, and was unreceptive to any advice from the actors.

-He was not allowed any input to the direction of his character, or the scripts.

-Eccles was under pressure to re-sign for Season Two before Rose even aired. During this time, his father was dying. With filming taking nine months straight, he didn't know if he would have the time to dedicate to another season.

-While he was deciding whether to stay or go, the BBC execs told RTD and Julie Gardner to start talking to David Tennant. Chris found out, and felt like he was no longer wanted. This is also about the same time the BBC came out and stated "typecasting" fears for his reason in leaving, which was a lie.

-Doctor Who suddenly became the BBC's flagship show, and they were trying to get this reclusive actor to do all of this press for the show.

I would say 90% of the above is steeped in truth. I don't think it was any one single reason...

Thing is, I have read/heard stuff where Eccleston said right from the start that he would probably only do one series, so I wouldnt take his word as gospel that it was all other peoples faults.
Also, he really isnt that good an actor, so thats why he was probably treated that way.