So the plot thickens, at least in the sense Eccleston has made more somewhat cryptic comments about his issues on-set. It now turns out his relationship with Russell T Davies wasn't exactly sparkly either.
As per the Radio Times' snippets from a larger interview
"My relationship with my three immediate superiors – the showrunner, the producer and co-producer – broke down irreparably during the first block of filming and it never recovered,"
"They lost trust in me, and I lost faith and trust and belief in them,"
"Some of my anger about the situation came from my own insecurity, ... They employed somebody [as the Doctor] who was not a natural light comedian."
"When I left, I gave my word to [then-showrunner] Russell T Davies that I wouldn’t do anything to damage the show ... But they did things to damage me. I didn’t criticise anybody."
It's hard to know exactly what he means, but I can't help but think my original assessment is close to the truth: that on the basis of previous 'serious drama' work with Davies, he took on the Dr. Who role, and blew a gasket when he realised it involved running around battling fart-monsters, and having a weird will-they-won't-they with his teenage travelling companion. I can totally appreciate that if comedic roles aren't ones forté you might bristle a little bit, and I guess Eccleston overreacted?
He says it all blew up during the 'first block' of filming, and I'm pretty sure that was indeed the pilot (complete with plastic Mickey [ooh err]), and the Slitheen episodes - definitely the first seasons daftest, outwardly ... zany, portion. Perhaps he burnt his bridges too spectacularly after that to row back.